GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00900 in Pseudomonas simiae WCS417

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF3277 PS417_16775 branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__WCS417:GFF3277
          Length = 255

 Score =  187 bits (474), Expect = 2e-52
 Identities = 101/249 (40%), Positives = 164/249 (65%), Gaps = 8/249 (3%)

Query: 2   AEKSNKVLLQVKGLKVAY-GGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTL- 59
           AE +++ LL V  ++V Y G I AV GV   V +G  V+L+G+NGAGK+TT+KAI+G + 
Sbjct: 6   AESASQALLSVNDIEVIYDGAILAVAGVSLSVPKGATVALLGANGAGKSTTLKAISGLVR 65

Query: 60  ----SMNDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRK-D 114
                ++ G IEY G  + G      V++G+V V EGR VF ++++ +NL+ G ++R+  
Sbjct: 66  AERAEVSRGTIEYAGTDLAGIDPSQRVRQGMVHVLEGRHVFGQLSVEDNLRSGGFVRRLS 125

Query: 115 KAGILADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLS 174
           +  +  D+E+++  FPRL+ ++   AG  SGGEQQM+A+GRALM++P ++LLDEPSMGL+
Sbjct: 126 RQEMEHDLERLYAWFPRLKTKRHTRAGLTSGGEQQMVAIGRALMTRPTLVLLDEPSMGLA 185

Query: 175 PIMVDKIFEVVRDV-YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDP 233
           P++V +IFE++  +     V+ ++ EQN + AL  A  GYV+++G + ++G   +LL   
Sbjct: 186 PMIVQEIFEIIGQLNREQQVSFLIAEQNINVALNYASHGYVLDTGRVALSGSAAELLARG 245

Query: 234 KVRAAYLGE 242
            +   YLG+
Sbjct: 246 DLHDIYLGK 254


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: 164
Number of extensions: 8
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: 242
Length of database: 255
Length adjustment: 24
Effective length of query: 218
Effective length of database: 231
Effective search space:    50358
Effective search space used:    50358
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