GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citA in Pseudomonas simiae WCS417

Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate GFF2854 PS417_14575 MFS transporter

Query= SwissProt::P0A2G3
         (434 letters)



>FitnessBrowser__WCS417:GFF2854
          Length = 445

 Score =  240 bits (613), Expect = 6e-68
 Identities = 153/437 (35%), Positives = 229/437 (52%), Gaps = 11/437 (2%)

Query: 3   QHTPATSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVF 62
           Q +P T R      I+    GNF+E FDF ++GF AT IA+ FFP+    A+L+ TFAVF
Sbjct: 8   QVSPQTLRK----VIIAAGIGNFVEWFDFAVYGFLATTIAQQFFPSGDASAALLKTFAVF 63

Query: 63  GSGFLMRPVGAIVLGAYIDRIGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLL 122
              F  RP+G I  G   DRIGR++ L +T+ +M   T LI L+P Y  IG+AAP L+ L
Sbjct: 64  AVAFAFRPLGGIFFGMLGDRIGRKRTLAMTILLMAGATTLIGLLPTYAAIGVAAPILLSL 123

Query: 123 GRLLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGH 182
            R  QGFSAG E  G   YL E A    + +Y S+   S   A   AA++ Y+L  +L  
Sbjct: 124 IRCAQGFSAGGEYAGACAYLMEHAPSDKRAWYGSFVPVSTFSAFAAAAVVAYALEASLSA 183

Query: 183 DAISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAF--LQRKHRPDTREIFATIAKNWRII 240
           +A+  WGWR+PF I   +  +   LR  L ET AF  ++ +H      +  T+  +   I
Sbjct: 184 EAMGSWGWRLPFLIAAPLGLVGLYLRWKLDETPAFQAVKEEHTVAHSPLKETLRNHGAAI 243

Query: 241 TAGTLLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLIVTMLVGVSNFIWLPIGGAISDR 300
           +     V++T  +FY  T Y  TY +    LS   +L+V+++  +      P+ G  SDR
Sbjct: 244 SCLGAFVSLTALSFYMFTTYFATYLQVAGGLSRAMALLVSLIALIFAAAICPLAGLYSDR 303

Query: 301 IGRRAVLMGITLLALITTWPVMQWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAA-LTEV 359
           +GRRA +M   +L ++  +P   +L A+      ++V +       +  G + AA L+E 
Sbjct: 304 VGRRATVMTACVLLMVVVYP--SFLMASSGSFAASIVGVMLLAVGAVLCGVVTAALLSET 361

Query: 360 MPVYVRTVGFSLAFSLATAIFGGLTPAISTALVKLTGDKSSPGWWLMCAALCGLAATAML 419
            P   R    ++ ++LA  IFGG  P ++T L+  TG   SP ++L+  AL  LA    L
Sbjct: 362 FPTRTRYTASAITYNLAYTIFGGTAPLMATWLISTTGSNLSPAFYLIAVALLALAGGLAL 421

Query: 420 --FVRLSRGYIAAENKA 434
               R+S   + AE+K+
Sbjct: 422 PETSRISLHDVGAEDKS 438


Lambda     K      H
   0.329    0.140    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: 496
Number of extensions: 17
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: 434
Length of database: 445
Length adjustment: 32
Effective length of query: 402
Effective length of database: 413
Effective search space:   166026
Effective search space used:   166026
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