GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citA in Sulfuricurvum kujiense DSM 16994

Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate WP_013459347.1 SULKU_RS02455 MFS transporter

Query= SwissProt::P0A2G3
         (434 letters)



>NCBI__GCF_000183725.1:WP_013459347.1
          Length = 409

 Score =  182 bits (463), Expect = 1e-50
 Identities = 112/401 (27%), Positives = 197/401 (49%), Gaps = 26/401 (6%)

Query: 23  GNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVFGSGFLMRPVGAIVLGAYIDR 82
           GN +E +DF L GF A  +   FFP+   F SL+ +F  F +G +MRPVGA++ G   DR
Sbjct: 14  GNVIEYYDFALIGFLAVMMGNLFFPSHDPFLSLLGSFGAFAAGMIMRPVGALIFGHIGDR 73

Query: 83  IGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLLGRLLQGFSAGVELGGVSVYL 142
           + RR  LM +L +M   T LI  +P Y  IG+ AP L++L R++QG S G E     VYL
Sbjct: 74  VSRRTALMSSLLMMALPTFLIGFLPTYAQIGILAPILLVLLRMIQGLSVGGEYASSIVYL 133

Query: 143 SEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGHDAISEWGWRIPFFIGCMIIP 202
            E + P ++  Y S+ S   ++ + + +    +L   +G DA+ EWGWRIPF+   +I  
Sbjct: 134 VEQSAPDHQNLYGSFVSVGAKIGMALGSGFCGALLWYIGGDAMGEWGWRIPFWASIIIAA 193

Query: 203 LIFVLRRSLQETEAFLQRKHRPDTREIFATIAKNWRIITAGTLLVAMTTTTFYFITVYTP 262
               LRR+L +     + K  P    +     + W+ +T  + +       +Y + +Y P
Sbjct: 194 AGLYLRRNLTDDYRPSEDKTVPIVAILRHHRREFWQFLTIASAIWVF----YYTVFIYLP 249

Query: 263 TYGRTVLNLSARDSLIVTMLVGVSNFIWLPIGGAISDRIGRRAVLMGITLLALITTWPVM 322
            +      LS  ++  +  L  V   +++P+   ++D IG   ++   ++   I+ +P+ 
Sbjct: 250 IWLEGSAGLSKAEAGQINTLSIVVGVVFIPLMAMVADVIGSLRLMRLTSITLAISVYPLF 309

Query: 323 QWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTV------GFSLAFSL- 375
            W++    +  +   +           G ++       P++  TV      G+  +F+  
Sbjct: 310 YWMSIGGFWGALAGTI-----------GLVILLCAFQAPIFASTVNALHYHGYRASFTAV 358

Query: 376 ----ATAIFGGLTPAISTALVKLTGDKSSPGWWLMCAALCG 412
               A  I GG+TPA+ T++ + +G+  +P + +  A+L G
Sbjct: 359 ILGSAAGIVGGITPALMTSITEYSGNPFAPSYLIAAASLMG 399


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: 471
Number of extensions: 20
Number of successful extensions: 3
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: 409
Length adjustment: 32
Effective length of query: 402
Effective length of database: 377
Effective search space:   151554
Effective search space used:   151554
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: 50 (23.9 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