GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Desulfovibrio vulgaris Hildenborough

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 206400 DVU0968 amino acid ABC transporter, ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>MicrobesOnline__882:206400
          Length = 246

 Score =  114 bits (285), Expect = 2e-30
 Identities = 78/249 (31%), Positives = 133/249 (53%), Gaps = 22/249 (8%)

Query: 6   ILTARGLVKRY---GRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGE 62
           I++AR + K +     + AL     D+ PGE++ +IG +G+GKS+ ++ ++     D GE
Sbjct: 3   IISARNVNKYFYVPEELHALRDVSLDVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADSGE 62

Query: 63  IRLEGKPI-QFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121
           I +EG+ I   +  +   +A +  V+Q+  L P LS+ +N+ L +            R  
Sbjct: 63  ILIEGRDILDPKCEINEVRAEVGMVFQSFNLFPHLSVLENVALAQMT---------VRKR 113

Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181
            RA  EK+    L+++G+     +    + LSGGQ+Q VA+AR+ A   K+++ DEPT+A
Sbjct: 114 SRAESEKKGMELLTKVGIADKHAVYP--DQLSGGQQQRVAIARSLAMDPKIMLFDEPTSA 171

Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241
           L  +    VL+++ ++ R G+ +V+++H M    EVADR+     G  L +  PKD    
Sbjct: 172 LDPEMVGEVLDVMRNLAREGMTMVVVTHEMGFAREVADRVVFMDHGAILEIATPKD---- 227

Query: 242 DAVAFMTGA 250
               F TGA
Sbjct: 228 ---LFTTGA 233


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: 155
Number of extensions: 7
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: 260
Length of database: 246
Length adjustment: 24
Effective length of query: 236
Effective length of database: 222
Effective search space:    52392
Effective search space used:    52392
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: 46 (22.3 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