GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Shewanella sp. ANA-3

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__ANA3:7026050
          Length = 376

 Score =  130 bits (327), Expect = 4e-35
 Identities = 83/250 (33%), Positives = 129/250 (51%), Gaps = 17/250 (6%)

Query: 10  LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69
           +++  ISK+FG  QALS + + I+ G++ GL+GP+G+GKTT   +I GL   D+G     
Sbjct: 3   IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFG 62

Query: 70  GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKA 129
            +  + T VH V    +   FQN  LF  MT  +NV            FG     K  + 
Sbjct: 63  NR--DVTQVH-VRDRRVGFVFQNYALFRHMTVADNV-----------AFGLEVIPKKQRP 108

Query: 130 EEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMN 189
            +A I KR   LL+ V +G  A      LS G ++R+ +ARALAT P+++ LDEP   ++
Sbjct: 109 SKAEIQKRVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALD 168

Query: 190 ATEKVQLRELIDRIRNDNR-TILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV--QK 246
           A  + +LR  +  + ++ + T + + HD    + L DRV V+  G       P E+  Q 
Sbjct: 169 AKVRKELRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQP 228

Query: 247 NEKVIEAYLG 256
           N + +  +LG
Sbjct: 229 NSRFVFDFLG 238


Lambda     K      H
   0.319    0.137    0.384 

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: 185
Number of extensions: 7
Number of successful extensions: 4
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: 260
Length of database: 376
Length adjustment: 27
Effective length of query: 233
Effective length of database: 349
Effective search space:    81317
Effective search space used:    81317
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 (21.7 bits)
S2: 48 (23.1 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