GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS32820 BPHYT_RS32820 xylose ABC
           transporter substrate-binding protein
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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