GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bglF in Tatumella morbirosei LMG 23360

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_052752467.1 HA49_RS10585 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000757425.2:WP_052752467.1
          Length = 467

 Score =  493 bits (1270), Expect = e-144
 Identities = 239/442 (54%), Positives = 327/442 (73%), Gaps = 8/442 (1%)

Query: 3   ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62
           +LA +IV  VGG +NI +++HCATRLRFKL       A  +K   G++ VVESGGQFQVV
Sbjct: 6   QLATQIVEAVGGKNNIQTVVHCATRLRFKLASTPLDAASKVKALEGVMAVVESGGQFQVV 65

Query: 63  IGNHVADVFLAVNSVAGLDEKAQQ-----APENDDKGNLLNRFVYVISGIFTPLIGLMAA 117
           IGNHV +VF A+      D + +Q     AP     G LL RF+ ++SGIFTP++G+MAA
Sbjct: 66  IGNHVGEVFRAIELFLAGDGEVRQDTDRTAPSKPAAG-LLARFIDLVSGIFTPVLGVMAA 124

Query: 118 TGILKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVI 177
           +G+LKG LALAL     +++SGTY I F+ASDALF+FFP++LGYTAGK+FGG+PF  M I
Sbjct: 125 SGMLKGFLALALALNLLSQESGTYQIWFAASDALFYFFPLVLGYTAGKKFGGSPFLTMAI 184

Query: 178 GGALVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAW 237
           GGALVHP+I++   NG    A+   F G+P+T +NYSSSVIPIIF++W C  LE++L   
Sbjct: 185 GGALVHPVIMS-LSNGSDPSAVDT-FFGLPLTFINYSSSVIPIIFASWACCWLEKQLYPR 242

Query: 238 LPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFW 297
           LPS+I+NF TPL CLMVI P+TFL++GPLST++S+ +A+GY W+Y   P  AG  +G  W
Sbjct: 243 LPSSIRNFATPLFCLMVIVPLTFLVIGPLSTFLSQCLASGYQWIYDIAPWIAGIFLGSVW 302

Query: 298 QIFVMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAG 357
           QI V+FGLHWGL+P+ INN ++LG+DT++PLL+PA++ Q GAALGVFL  ++ + K++AG
Sbjct: 303 QICVIFGLHWGLIPVAINNLSMLGFDTIVPLLLPAVLGQTGAALGVFLACKEQKLKMLAG 362

Query: 358 SAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQ 417
           ++    LFGITEPA+YGV LP + PF++ CI+G +G  I+G  Q KV+SFGL S+F+F Q
Sbjct: 363 TSVTAGLFGITEPAIYGVTLPLRKPFMMGCIAGGIGGGIVGLFQAKVWSFGLVSVFSFTQ 422

Query: 418 TIPSTGIDFTVWASVIGGVIAI 439
            IP+ G+D +VW +V+G + A+
Sbjct: 423 MIPAEGVDLSVWGAVVGAITAL 444


Lambda     K      H
   0.324    0.141    0.427 

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: 1059
Number of extensions: 65
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: 625
Length of database: 467
Length adjustment: 35
Effective length of query: 590
Effective length of database: 432
Effective search space:   254880
Effective search space used:   254880
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 (21.5 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