GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Azospirillum brasilense Sp245

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS22325 AZOBR_RS22325 branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__azobra:AZOBR_RS22325
          Length = 286

 Score =  218 bits (556), Expect = 8e-62
 Identities = 117/240 (48%), Positives = 167/240 (69%), Gaps = 9/240 (3%)

Query: 9   LLQVKGLKVAYGGIQAV-KGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDG--- 64
           LL V  ++V Y  +  V +G+  EV EGE+V+L+G+NGAGK+TT+KAI+G L   DG   
Sbjct: 27  LLSVNNIEVVYNDVILVLRGLSLEVPEGEIVALLGANGAGKSTTLKAISGLLKTEDGEVT 86

Query: 65  --NIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADI 122
             +I + G+ I G     +V+ G+  V EGR +   MT  ENL++GA+ R+D  G+  DI
Sbjct: 87  RGDISFAGERINGIDPDKIVRRGIFQVMEGRRIIGDMTCQENLRLGAFTRRD-GGVKDDI 145

Query: 123 EKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIF 182
           E ++  FPRL+ER   LAG +SGGEQQMLA+GRA+M++PK++L+DEPSMGLSP+MV ++F
Sbjct: 146 EMVYHYFPRLKERTG-LAGYLSGGEQQMLAIGRAMMARPKLILMDEPSMGLSPLMVKEVF 204

Query: 183 EVVRDVYA-LGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
            ++R +   LGVTI+LVEQNA  AL  A RGY+ME+G + + G  ++L N+  V+  YLG
Sbjct: 205 SIIRQINKDLGVTILLVEQNARMALQAATRGYIMENGKVVLDGTAEELRNNEDVKEFYLG 264


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: 199
Number of extensions: 10
Number of successful extensions: 5
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: 286
Length adjustment: 25
Effective length of query: 217
Effective length of database: 261
Effective search space:    56637
Effective search space used:    56637
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: 47 (22.7 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