GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Shewanella loihica PV-4

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  201 bits (511), Expect = 3e-56
 Identities = 106/253 (41%), Positives = 162/253 (64%), Gaps = 9/253 (3%)

Query: 4   IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63
           +++E +SK+F     +V+AVD+VS+ I+ G  F +LG SG GK+T LR++AG E+PT G 
Sbjct: 21  LKIERVSKLFD----DVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGR 76

Query: 64  IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123
           IY D + ++      M P +R I M+FQ++AL+P+MTV  NIAF LK  K+PK +IE +V
Sbjct: 77  IYLDGQDITD-----MPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRV 131

Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183
           KE+ + + +     R P +LSGGQ QR A+AR+L K PK+LLLDEP   LD ++R   + 
Sbjct: 132 KEMLKLVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQL 191

Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243
            V  I     +T ++V+HD  +   +A +  ++ +G  AQ G+P +IYE PA  ++A   
Sbjct: 192 EVVDILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFI 251

Query: 244 GEINLIQAKIIEN 256
           G +NL +  I+E+
Sbjct: 252 GSVNLFEGDIVED 264


Lambda     K      H
   0.317    0.136    0.374 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 287
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 371
Length of database: 378
Length adjustment: 30
Effective length of query: 341
Effective length of database: 348
Effective search space:   118668
Effective search space used:   118668
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory