GapMind for catabolism of small carbon sources

 

Aligments for a candidate for citA in Cupriavidus basilensis 4G11

Align citrate transporter (characterized)
to candidate RR42_RS07875 RR42_RS07875 citrate-proton symporter

Query= CharProtDB::CH_014606
         (431 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS07875 RR42_RS07875
           citrate-proton symporter
          Length = 433

 Score =  553 bits (1424), Expect = e-162
 Identities = 262/417 (62%), Positives = 329/417 (78%)

Query: 1   MTQQPSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFG 60
           M+  PS+   F  + RV SGNFLE +DF ++GFYA  IAKTFFP+ +EFA+LML+ A FG
Sbjct: 1   MSSSPSQQHGFRTVFRVVSGNFLEMYDFMVYGFYAAAIAKTFFPSGNEFASLMLSLATFG 60

Query: 61  SGFLMRPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVG 120
           +GFLMRP+GA++LGAYID  GRRKGL++TL +M  GTLLIA VPGY +IG+ AP+LVL G
Sbjct: 61  AGFLMRPLGAIILGAYIDHHGRRKGLIMTLVLMALGTLLIACVPGYASIGVAAPLLVLAG 120

Query: 121 RLLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHD 180
           RLLQGFSAGVELGGVSVYL+EIA PG KGFY +WQSASQQVA++ A L+G  L+  L  +
Sbjct: 121 RLLQGFSAGVELGGVSVYLAEIAKPGKKGFYVAWQSASQQVAVIFAGLLGVVLHSMLSPE 180

Query: 181 EISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAG 240
           E+ EWGWRIPF IGC+I+P +F++RRSL+ETE F  RKHRP   EI+ ++ +NWRII AG
Sbjct: 181 EMGEWGWRIPFLIGCLIVPFLFLIRRSLEETEEFKTRKHRPSISEIYRSMMENWRIIVAG 240

Query: 241 TLLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGR 300
            ++V MTT +FY IT YTPT+G+TVL L   D+L+VTM VG+SNFIWLP+ GA+SDR+GR
Sbjct: 241 CMMVVMTTVSFYMITAYTPTFGKTVLKLDDVDNLIVTMCVGLSNFIWLPLMGALSDRVGR 300

Query: 301 RPVLMGITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVY 360
           +P+L+  T+L L+T  P ++WL A P F R+ +V LW SF +G YNGAMV  LTEVMP  
Sbjct: 301 KPLLVIFTILTLLTAYPAVSWLVAEPSFGRLLMVELWLSFLYGSYNGAMVVTLTEVMPPA 360

Query: 361 VRTVGFSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLF 417
           VRT GFSLA+SLATA+FGG TPAIST L+  TG+K++PG WLM AA CGL AT ++F
Sbjct: 361 VRTAGFSLAYSLATALFGGFTPAISTYLIHSTGNKAAPGLWLMFAAACGLIATLVIF 417


Lambda     K      H
   0.328    0.141    0.432 

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: 601
Number of extensions: 19
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: 431
Length of database: 433
Length adjustment: 32
Effective length of query: 399
Effective length of database: 401
Effective search space:   159999
Effective search space used:   159999
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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