GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Galbibacter marinus ck-I2-15

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_008990494.1 I215_RS03100 D-xylose transporter XylE

Query= TCDB::P15729
         (468 letters)



>NCBI__GCF_000300875.1:WP_008990494.1
          Length = 543

 Score =  292 bits (747), Expect = 2e-83
 Identities = 182/432 (42%), Positives = 261/432 (60%), Gaps = 38/432 (8%)

Query: 51  TDSLLTGLSVSLALLGSALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLP-----F 105
           T+S+L G  VS AL+G  +GA     +A+  GR   +++AA LF +S+ GSG P     F
Sbjct: 121 TNSIL-GFMVSSALVGCIIGASLGDRVANSVGRRNGLLIAAFLFFISAAGSGYPELLNPF 179

Query: 106 TIWD---FIFWRVLGGIGVGAASVIAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLS 162
           +  D   FI +R++GGIGVG AS++AP YIAE++PA++RG+L S  QLAIV G+ I    
Sbjct: 180 SSGDLSTFIVYRIIGGIGVGLASMLAPLYIAEMAPANIRGKLVSCNQLAIVGGMLIVYFV 239

Query: 163 NWFIALMAGGSAQNPWLFGAAAWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKA 222
           N+FI  + G S Q  W+     WR+MF +E IPA+L+ +  F +P++PR+ V +G  E A
Sbjct: 240 NYFI--VKGQSDQ--WI-NTIGWRYMFLSECIPAVLFLISLFFVPKTPRFQVLKGNDEAA 294

Query: 223 AAILWKVEGGDVPSRIEEIQATVSLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGI 282
              L K  G   PS+   I   +    K + +  LS   G   I+ IG+ LS  QQFVGI
Sbjct: 295 IETLTKYNG---PSKASLILTEIKRSFKIKKAPWLSYGWG---IIIIGLLLSVFQQFVGI 348

Query: 283 NVIFYYSSVLWRSVGFTEEKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMT 342
           NV+ YY+  +++ +G   + S+L T+I G IN++ T++AI  VDKFGRK L+ +GS+ M 
Sbjct: 349 NVVLYYAPEIFKGMGMKTDASMLQTIIVGIINLIFTVIAIFTVDKFGRKKLMFIGSVIMA 408

Query: 343 ITLGILSVVFGGATVVNGQPTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNK 402
           +++       G  TV+  Q T     G+ AL+   LY+ +F  SWGP+ WVLL E+F NK
Sbjct: 409 VSM------IGLGTVLYSQDT-----GMAALLLMLLYIAAFAVSWGPVTWVLLSEIFPNK 457

Query: 403 IRAAALSVAAGVQWIANFIISTTFPP------LLDTVGLGPAYGLYATSAAISIFFIWFF 456
           I+  A+++A  VQW+AN ++S TFP       L +T   G AY +Y   A +S  FI  F
Sbjct: 458 IK-GAMAIAVAVQWLANLLVSWTFPMMNNNTYLTETFHNGFAYWVYGIMAVLSGIFILKF 516

Query: 457 VKETKGKTLEQM 468
           V ETKGKTLE+M
Sbjct: 517 VPETKGKTLEEM 528


Lambda     K      H
   0.325    0.140    0.430 

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: 661
Number of extensions: 36
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 468
Length of database: 543
Length adjustment: 34
Effective length of query: 434
Effective length of database: 509
Effective search space:   220906
Effective search space used:   220906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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