GapMind for catabolism of small carbon sources

 

Alignments for a candidate for chvE in Brucella inopinata BO1

Align CVE1 aka ChvE aka ATU2348 aka AGR_C_4267, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_008509253.1 BIBO1_RS15350 D-xylose ABC transporter substrate-binding protein

Query= TCDB::P25548
         (354 letters)



>NCBI__GCF_000182725.1:WP_008509253.1
          Length = 339

 Score =  174 bits (442), Expect = 2e-48
 Identities = 113/342 (33%), Positives = 175/342 (51%), Gaps = 21/342 (6%)

Query: 9   AACAIGAASFAAPAFAQDKGSVGIAMPTKSSARWIDDGNNIVKQLQEAGYKTDLQYADDD 68
           AA  IGA      + + +   +G ++      RW  D +  +   ++ G K ++Q AD +
Sbjct: 14  AALGIGAMGATPASASPEHPVIGFSIDDLRVERWARDRDYFIAAAEKLGAKVNVQSADGN 73

Query: 69  IPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRNSGDVSYYA 128
              Q+ Q+EN++++GV  +VI  ++      V+  A   GIKV++YDRLI N+ D+  Y 
Sbjct: 74  EEKQVKQVENLISQGVDAIVIVPMNSKVFDAVVADAKASGIKVLSYDRLILNA-DIDAYI 132

Query: 129 TFDNFQVGVLQATSITDKLGLKDGKGPFNIELFGGSPDDNNAFFFYDGAMSVLKPYIDSG 188
           +FDN +VG +QA ++         K   N  L GGSP DNNA     G    LK  +DSG
Sbjct: 133 SFDNERVGFMQAQAVL------KAKPEGNYYLLGGSPTDNNAKLLRAGQEKALKEAVDSG 186

Query: 189 KLVVKSGQMGMDKVGTLRWDPATAQARMDNLLSAYYTDAKVDAVLSPYDGLSIGIISSLK 248
           K+ +   Q          W P  A + M+N L+A  T  K+DAV++  DG + G I +L 
Sbjct: 187 KVKIVGSQW------VKEWSPTEALSIMENALTA--TQNKIDAVVASNDGTAGGAIQALA 238

Query: 249 GVGYGTKDQPLPVVSGQDAEVPSVKSIIAGEQYSTIFKDTRELAKVTVNMVNAVMEGKEP 308
             G   K      VSGQD+++ +VK ++ G Q  T++K  + +A+    +   ++  ++P
Sbjct: 239 AQGLAGK----TAVSGQDSDLAAVKRLVDGTQTVTVYKPLKLIAEEAAKLTVQLVRDEKP 294

Query: 309 EVNDTKTYENGVKVVPSYLLKPVAVTKENYKQVLVDGGYYKE 350
           E N      NG K V + LL P AVTK+N    + DG Y KE
Sbjct: 295 EFNG--KINNGSKDVDTLLLTPTAVTKDNIDIYIKDGFYTKE 334


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: 329
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: 339
Length adjustment: 29
Effective length of query: 325
Effective length of database: 310
Effective search space:   100750
Effective search space used:   100750
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 24 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