GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlK in Shewanella sp. ANA-3

Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_25895
         (367 letters)



>lcl|FitnessBrowser__ANA3:7026050 Shewana3_3192 sulfate ABC
           transporter, ATPase subunit (RefSeq)
          Length = 376

 Score =  212 bits (539), Expect = 2e-59
 Identities = 104/236 (44%), Positives = 159/236 (67%), Gaps = 4/236 (1%)

Query: 4   LKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELD 63
           +++ N+ K F  F  +  ++L++ + E +  +GPSG GK+TLLR+IAGLE   +G I   
Sbjct: 3   IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFG 62

Query: 64  GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGV----NKAEVEKKVNEAAR 119
            RD+T+V    R +  VFQ YAL+ HM+V  N++F L++       +KAE++K+V+    
Sbjct: 63  NRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLE 122

Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179
           +++LG + +R P+QLSGGQ+QR+A+ RA+   P++ L DEP   LDA +R ++R  L  L
Sbjct: 123 MVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSL 182

Query: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLG 235
           H EL+ T ++VTHDQ EA+ L+D+VVV++ G IEQV +P+ELY QP + FV  FLG
Sbjct: 183 HDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLG 238


Lambda     K      H
   0.321    0.137    0.390 

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: 333
Number of extensions: 18
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 367
Length of database: 376
Length adjustment: 30
Effective length of query: 337
Effective length of database: 346
Effective search space:   116602
Effective search space used:   116602
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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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