GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS07875
          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:

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