GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcA in Shewanella sp. ANA-3

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 7023263 Shewana3_0497 ABC transporter related (RefSeq)

Query= SwissProt::Q9F9B0
         (260 letters)



>lcl|FitnessBrowser__ANA3:7023263 Shewana3_0497 ABC transporter
           related (RefSeq)
          Length = 348

 Score = 96.3 bits (238), Expect = 8e-25
 Identities = 71/224 (31%), Positives = 114/224 (50%), Gaps = 18/224 (8%)

Query: 7   LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66
           + A GL KRY    AL    F+L+ G+ LA++G NGAGKS++IK I G V+P +GE+ ++
Sbjct: 29  IKAIGLCKRYATFEALTDLHFELHAGQTLALLGHNGAGKSTLIKMILGLVSPSQGELFVQ 88

Query: 67  GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126
           G+P+      +   A +   Y    L   +S  DNM   +EI        +F  L +   
Sbjct: 89  GQPLH----TKRANANLSLGY----LPENVSFYDNM-TAQEIL------SYFAKL-KGVA 132

Query: 127 EKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKE 186
            K+    L E GLM  +  ++ + T S G RQ + +A+A     KV+++DEPT  L    
Sbjct: 133 PKRVSILLEEFGLMAAK--DKRLSTFSKGMRQRLGLAQAVLADPKVLLLDEPTVGLDPLA 190

Query: 187 SRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRL 230
           S  + + +  ++ +G  I++ +H +  V +  D   I   GR L
Sbjct: 191 SAFLYQKMAQLKAQGCAIIISTHELGLVQDQMDSALILGQGRLL 234


Lambda     K      H
   0.321    0.136    0.383 

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: 162
Number of extensions: 6
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: 260
Length of database: 348
Length adjustment: 27
Effective length of query: 233
Effective length of database: 321
Effective search space:    74793
Effective search space used:    74793
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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