GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Shewanella amazonensis SB2B

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q97UF2
         (371 letters)



>FitnessBrowser__SB2B:6939439
          Length = 370

 Score =  143 bits (360), Expect = 9e-39
 Identities = 81/243 (33%), Positives = 132/243 (54%), Gaps = 7/243 (2%)

Query: 17  KTEVKAVDNVSITID----SGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEA-V 71
           + +++    + I  D    +G    V+GPSG GKTT LR+IAGL +P +G I        
Sbjct: 8   RVQIRQTKGIRIEADFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWF 67

Query: 72  SSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEELG 131
            S   +  SP+ R I  V Q++ L+P ++   NI   L    +P  +   +     E++ 
Sbjct: 68  DSDEGIHCSPQNRHIGFVPQHFGLFPKLSALGNIMAALD--HLPSQERRPRALAALEKVN 125

Query: 132 LSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRE 191
           L G+ +R P +LSGGQ QR A+ARAL ++P+VLLLDEPFS +D + RE     + +++ E
Sbjct: 126 LHGLTDRLPSQLSGGQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAE 185

Query: 192 RKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGEINLIQA 251
             +  ++V+HD  +   +A+   +I  G   Q GTP +++  P  + +AR  G  N+  A
Sbjct: 186 LNIPVIMVTHDLNEALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAVARQMGLRNIFNA 245

Query: 252 KII 254
            ++
Sbjct: 246 HVV 248


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: 240
Number of extensions: 9
Number of successful extensions: 3
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: 370
Length adjustment: 30
Effective length of query: 341
Effective length of database: 340
Effective search space:   115940
Effective search space used:   115940
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: 49 (23.5 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