GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Pseudomonas simiae WCS417

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF525 PS417_02675 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__WCS417:GFF525
          Length = 238

 Score =  228 bits (580), Expect = 1e-64
 Identities = 123/233 (52%), Positives = 163/233 (69%), Gaps = 1/233 (0%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +L++K L V YG IQA+K V   + EGE VSLIGSNGAGK+T + +I G      G I Y
Sbjct: 5   ILEMKDLDVYYGPIQALKKVSLHINEGETVSLIGSNGAGKSTLLMSIFGQPRAESGQILY 64

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128
            G  I  K +  +   G+   PEGR VF  MT+ ENL MG     DK     D+++MF +
Sbjct: 65  NGVDITHKSSHYIASNGIAQSPEGRRVFPDMTVEENLLMGTIPIGDKFA-QEDMQRMFEL 123

Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188
           FPRL+ER++Q A TMSGGEQQMLA+ RALMS+PK+LLLDEPS+GL+PI+V +IF  +R++
Sbjct: 124 FPRLKERRNQRAMTMSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFSTLREL 183

Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
            + G+TI LVEQNA+ AL ++DR YVM +G I +TG G++LL + +VR AYLG
Sbjct: 184 ASTGMTIFLVEQNANHALRLSDRAYVMVNGEIRLTGTGKELLVNEEVRNAYLG 236


Lambda     K      H
   0.317    0.136    0.373 

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: 173
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: 242
Length of database: 238
Length adjustment: 23
Effective length of query: 219
Effective length of database: 215
Effective search space:    47085
Effective search space used:    47085
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: 46 (22.3 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