GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citA in Rhizobium etli CFN 42

Align citrate transporter (characterized)
to candidate WP_011427276.1 RHE_RS20930 MFS transporter

Query= CharProtDB::CH_014606
         (431 letters)



>NCBI__GCF_000092045.1:WP_011427276.1
          Length = 628

 Score =  171 bits (434), Expect = 5e-47
 Identities = 99/312 (31%), Positives = 166/312 (53%), Gaps = 11/312 (3%)

Query: 20  GNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLMRPIGAVVLGAYIDR 79
           G   E +DF+L+G  ATYI  T+F    E    + T   F +GFL+RP GA+V G   D 
Sbjct: 29  GTVFEWYDFYLYGSLATYIGATYFTQYPEATRNIFTLLAFAAGFLVRPFGALVFGRLGDL 88

Query: 80  IGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQGFSAGVELGGVSVYL 139
           +GR+   ++T+ IMG  T L+ ++PG  +IG+ AP++++  RLLQG + G E GG + Y+
Sbjct: 89  VGRKYTFLVTILIMGMSTFLVGILPGAASIGIAAPIILIGLRLLQGLALGGEYGGAATYV 148

Query: 140 SEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEWGWRIPFFIGCMIIP 199
           +E A  G +G++TSW   +  + + ++ ++   +   +   + + WGWRIPF +  +++ 
Sbjct: 149 AEHAPNGRRGYFTSWIQTTATLGLFLSLIVIILVQSLMAPAQFAAWGWRIPFLVSVVLLG 208

Query: 200 LIFVLRRSLQETEAFLQRKHRPDTREIFTTIA----KNWRIITAGTLLVAM-TTTTFYFI 254
           +   +R  + E+ AF + K      +   T A    KN +I     L   M     +Y  
Sbjct: 209 ISVWIRLKMNESPAFQRMKAEGKGSKAPLTEAFGQWKNAKIALIALLGATMGQAVVWYGG 268

Query: 255 TVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLP---IGGAISDRIGRRPVLMGITLLA 311
             Y   + + VL +   D     ++V I+ F+  P   I G +SD+IGR+P++M   L+A
Sbjct: 269 QFYALFFLQNVLKV---DLFSANVMVAIALFLGTPFFVIFGGLSDKIGRKPIIMAGLLIA 325

Query: 312 LVTTLPVMNWLT 323
            VT  P+   +T
Sbjct: 326 AVTYNPLFKAMT 337



 Score = 40.0 bits (92), Expect = 2e-07
 Identities = 20/61 (32%), Positives = 29/61 (47%)

Query: 334 VLLWFSFFFGMYNGAMVAALTEVMPVYVRTVGFSLAFSLATAIFGGLTPAISTALVQLTG 393
           +L     +  M  G + A L E+ P  +R  G SL + +    FGGL PA + A+    G
Sbjct: 533 ILFVLVLYVTMVYGPIAALLVELFPTRIRYTGMSLPYHIGNGWFGGLLPATAFAMSAAAG 592

Query: 394 D 394
           D
Sbjct: 593 D 593


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: 639
Number of extensions: 38
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 431
Length of database: 628
Length adjustment: 35
Effective length of query: 396
Effective length of database: 593
Effective search space:   234828
Effective search space used:   234828
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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