A. NCBI blast server protein-protein blast
Results

B. BCM search launcher
Results

What additional information do you receive from each server?

NCBI

Only gives link to entrez sequence information
(DYI3_ANTCR > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=02494216&dopt=GenPept )
Entrez entry gives the sequence and Sequence annotations. See Info on WD repeat regions.

BCM

Blocks, Prodom, Prosite, Protein ID links to entrez (DYI3_ANTCR > http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&dopt=g&db=p&uid=2494216 )
Entrez entry gives the sequence and Sequence annotations. See Info on WD repeat regions.

Ic140  		~450 aa
Dyi3-antcr  	~600 aa
Dyi2-rat  	~640 aa
Dyin-dicdi  	~650 aa

PISE Clustal W | local

Results

In time will be able to link directly to boxshade, etc.

BCM clustal w

Results

Generate Boxshade image.
Review the alignment in the Jalview editor.

As read from the entrez sequence information page.

used lasergene seqedit to trim

ic140 		1 - 450  (+20 aa both ends)
Dyi3-antcr 	159 - 488
Dyi2-rat	277-607 (6)  - 650 (7)
Dyin-dicdi	276-620

PISE Clustal W | local

results

In time will be able to link directly to boxshade, etc.

BCM clustal w

Results

Generate Boxshade image.
Review the alignment in the Jalview editor.

A. COMPARE multiple alignment with trimmed sequences to the multiple alignment of the untrimmed sequences.

B. Also compare the results from the trimmed alignments to the alignments seen for the families below.

C. Compare the alignments of the dyneins without IC140.

Results
Did having IC140 in the alignment, change the alignment between the dyneins?

BLOCKS

Get blocks by number
BL00678

PROSITE

PS00678, PS50082, PS50294, PDOC00574

PRODOM

Prodom by id
PD000061

Prodom by blast
Submitted dyi2-antcr 140 - 510 ( note numbers will be off by 140)

Results

Prodom blast
ProDom domains producing High-scoring Segment Pairs:

  Position   ProDom domain                                    Score   E value
 
     1-67    #PD037574  REPEAT DYNEIN D CHAIN                     357  5e-35
    24-167   #PD433156  REPEAT D LARVAE GIANT                      80  0.007
    38-206   #PD414008  REPEAT CG7051 D CG13930                   100  3e-05
    60-105   #PD360226  REPEAT INNER DYNEIN D                     114  8e-07
    60-105   #PD000061                                             85  0.002
    68-151   #PD019187  REPEAT D DYNEIN CHAIN                     467  9e-48
    69-152   #PD407094  REPEAT DYNEIN D MOTOR                     262  5e-24
    77-152   #PD340580  REPEAT DYNEIN D INTERMEDIATE               83  0.003
   153-252   #PD388109  DYNEIN INTERMEDIATE CHAIN REPEAT           82  0.004
   153-214   #PD395110  REPEAT DYNEIN D CHAIN                     323  5e-31
   220-295   #PD019187  REPEAT D DYNEIN CHAIN                     433  8e-44
   224-295   #PD040521  REPEAT D DYNEIN INNER                     264  3e-24
   245-296   #PD000061                                            106  7e-06
   263-296   #PD407269  REPEAT D D-40 AT2G20330/F11A3.12           95  1e-04
   296-371   #PD129347  REPEAT DYNEIN D CHAIN                     286  9e-27

PD19187

500+ sequences
90 aa in length.  (note a single blade is ~ 40 aa)
Dyi3-antcr present.

PD037574	140 - 206	(REPEAT DYNEIN WD CHAIN)
PD19187		207 - 290	(REPEAT DYNEIN WD CHAIN)
PD395110	292 - 353	(REPEAT DYNEIN WD CHAIN)
PD19187		359 - 434	(REPEAT DYNEIN WD CHAIN)
PD129347	435 - 510	(REPEAT DYNEIN WD CHAIN)

PFAM
PFAM family 0040
(linked from Prodom)
seed 1930 sequences, whole family is 9117.

DYI2_antcr	372 - 411
		421 - 463
		529 - 568
		573 - 611
		only found 4 blades.  Each blade is  ~ 40 aa.

Review the alignment in the Jalview editor.

NOTE: There are multiple places to use each of the following. See that you have used them in at least one place. See the features and advantages of each.

boxshade
logos
Results
Jalview