GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Desulfacinum infernum DSM 9756

Align TreV, component of Trehalose porter (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  239 bits (610), Expect = 8e-68
 Identities = 127/311 (40%), Positives = 186/311 (59%), Gaps = 17/311 (5%)

Query: 1   MTVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60
           M +E+ D+ K YG+   + G++  +E G+  VILGPSG GK+TLL+++AG+E +  G I 
Sbjct: 1   MQIEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIH 60

Query: 61  ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120
             G D+T  PP KRN++MVFQ+YAL+P+++VR+NI F LK+R +  +EI  R+++   LL
Sbjct: 61  IAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLL 120

Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180
           G+S  LD K  ++SGG QQRVAL RAI+      L+DEPLSNLDA++R + R E+  +Q+
Sbjct: 121 GLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQR 180

Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNF 240
            L  T IYVTHDQ EA+++ADRI ++  G+  Q   P+  YE P   +VA+F+G  PMN 
Sbjct: 181 RLGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNI 240

Query: 241 LP-------------GEL----MKEKAQEIGFRPEWVEVGKGNLSCMVESVEASGESRYL 283
           +P             G L    M       G RPE + + +     MV   E  G   ++
Sbjct: 241 VPLCPTQGGAALEPGGRLLFPGMDPDRYLFGIRPENLRLAESGQPAMVTGREYLGSDTFV 300

Query: 284 ICNFKNNNITI 294
            C      + +
Sbjct: 301 SCEIHGQEVIV 311


Lambda     K      H
   0.318    0.137    0.385 

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: 278
Number of extensions: 11
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: 324
Length of database: 365
Length adjustment: 29
Effective length of query: 295
Effective length of database: 336
Effective search space:    99120
Effective search space used:    99120
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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