GapMind for catabolism of small carbon sources

 

Alignments for a candidate for chvE in Burkholderia phytofirmans PsJN

Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BPHYT_RS32820 BPHYT_RS32820 xylose ABC transporter substrate-binding protein

Query= TCDB::P25548
         (354 letters)



>FitnessBrowser__BFirm:BPHYT_RS32820
          Length = 342

 Score =  181 bits (459), Expect = 2e-50
 Identities = 121/350 (34%), Positives = 190/350 (54%), Gaps = 24/350 (6%)

Query: 6   SLMAACAIGAASFAAPAF--AQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYKTDLQ 63
           SL+    + + S  AP    ++D   +G  +      RW  D +  V   ++ G K  +Q
Sbjct: 12  SLVCGAVLASLSLVAPLAHASKDHPEIGFCIDDLRVERWSRDRDYFVAAAEKLGAKVSVQ 71

Query: 64  YADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNSGD 123
            AD     Q+SQIEN++++GV V+VI   +  TL +V+ +A + GIKV++YDRLI ++ D
Sbjct: 72  SADASEARQISQIENLISRGVDVIVIVPFNSKTLGNVVAEAKKAGIKVVSYDRLILDA-D 130

Query: 124 VSYYATFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVLKP 183
           V  Y +FDN +VG LQA       G+ + +   N  L GG+P DNNA    +G + +LKP
Sbjct: 131 VDAYISFDNEKVGELQAQ------GVYNAQPKGNYFLLGGAPTDNNAKMLREGQLKILKP 184

Query: 184 YIDSGKLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSIGI 243
            ID G + V   Q          W  +TA   +++ L+A   + K+DA+++  DG + G 
Sbjct: 185 AIDKGDIKVVGQQW------VPEWSASTALRIVEDALTA--NNNKIDAIVASNDGTAGGA 236

Query: 244 ISSLKGVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNAVM 303
           I +L       K   +P VSGQDA++ +VK +IAG Q  T++K  + +A     +  A+ 
Sbjct: 237 IQALAAQHMAGK---VP-VSGQDADLAAVKRVIAGTQTMTVYKPLKLIAGEAAKLSVALA 292

Query: 304 EGKEPEVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKEDQL 353
           +G++P  N    Y+NG K V + LL+P  +TK N   V+V  G+Y + QL
Sbjct: 293 KGEKPAFN--SQYDNGKKKVDTVLLQPTLLTKSNV-DVVVKDGFYSQAQL 339


Lambda     K      H
   0.314    0.133    0.372 

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: 301
Number of extensions: 17
Number of successful extensions: 6
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: 354
Length of database: 342
Length adjustment: 29
Effective length of query: 325
Effective length of database: 313
Effective search space:   101725
Effective search space used:   101725
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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