GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Shewanella amazonensis SB2B

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q88P35
         (384 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  216 bits (551), Expect = 6e-61
 Identities = 121/288 (42%), Positives = 178/288 (61%), Gaps = 6/288 (2%)

Query: 4   LELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAIL 63
           L++  V+K +       + D+ L+I  GE   L+G SG GKSTL+  +AG E+ T G I 
Sbjct: 21  LKIERVSKLFDD--VRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIY 78

Query: 64  IDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVAKLL 123
           +D QD++ + P +R I M+FQSYAL+P M+V +NI FGLK  K+ +A I + V  + KL+
Sbjct: 79  LDGQDITDLPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLV 138

Query: 124 QIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
            +E    RKP QLSGGQ+QRVA+ R+LA+RPK+ L DEP+  LD KLR +M+ E+  + +
Sbjct: 139 HMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILE 198

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPPMNF 243
           R+  T V VTHDQ EAMT+  ++A+M DG I Q G+P  IY  P ++ +A FIG+  +N 
Sbjct: 199 RVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGT--VNL 256

Query: 244 IPVRLARQDGRLLALLDSGQARCELPLGE-AADALEGREIILGIRPEQ 290
               +  +D    A+L S        +G     +LE + + L +RPE+
Sbjct: 257 FDCEII-EDEADHAILKSPTLPQPFLIGHGVTTSLEDKHVWLAVRPEK 303


Lambda     K      H
   0.320    0.137    0.391 

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: 314
Number of extensions: 8
Number of successful extensions: 1
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: 384
Length of database: 378
Length adjustment: 30
Effective length of query: 354
Effective length of database: 348
Effective search space:   123192
Effective search space used:   123192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

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

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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