GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Shewanella amazonensis SB2B

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  222 bits (566), Expect = 1e-62
 Identities = 123/308 (39%), Positives = 186/308 (60%), Gaps = 3/308 (0%)

Query: 23  NIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIMIGDQDVSGMSPKDRDIAMV 82
           ++ L+I +GE   L+G SG GKSTL+  +AG E  T G I +  QD++ + P +R I M+
Sbjct: 38  DVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLDGQDITDLPPYERPINMM 97

Query: 83  FQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLLQIEHLLNRKPGQLSGGQQQ 142
           FQSYAL+P M+V +NI FGLK  KM +ADI   V  + KL+ +E    RKP QLSGGQ+Q
Sbjct: 98  FQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHMEQYAKRKPHQLSGGQRQ 157

Query: 143 RVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAMTL 202
           RVA+ R+LA+RPK+ L DEP+  LD KLR +M+ E+  + +R+  T V VTHDQ EAMT+
Sbjct: 158 RVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTM 217

Query: 203 GDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNFVPLRLQRKDGRLVALLDSG 262
             ++A+M DG I Q G+P +IY +P ++ +A FIG+  +N     +   +     L    
Sbjct: 218 AGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGT--VNLFDCEIIEDEADHAILKSPT 275

Query: 263 QARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSASS-IRAEVQVTEPTGPDTLVF 321
             +  L  +     LED+ V L +RPE+ ++   + +   +  R +V      G  ++ +
Sbjct: 276 LPQPFLIGHGVTTSLEDKHVWLAVRPEKTLITREQPEGEYNWARGKVHDIAYLGGLSVYY 335

Query: 322 VQLNDTKV 329
           ++L D K+
Sbjct: 336 IKLEDDKI 343


Lambda     K      H
   0.318    0.135    0.382 

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: 305
Number of extensions: 7
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: 386
Length of database: 378
Length adjustment: 30
Effective length of query: 356
Effective length of database: 348
Effective search space:   123888
Effective search space used:   123888
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 (21.7 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