GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bglF in Bacillus safensis FO-36b

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_034281372.1 BA81_RS07465 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000691165.1:WP_034281372.1
          Length = 635

 Score =  462 bits (1189), Expect = e-134
 Identities = 253/628 (40%), Positives = 379/628 (60%), Gaps = 23/628 (3%)

Query: 3   ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62
           + A++++  VGG  N+  + HC TRLRF L DESKA  E L+ T G++ V +SGGQ+ V+
Sbjct: 5   QTAKEVLELVGGEKNVKQVTHCMTRLRFNLYDESKADKEKLQSTDGVMGVNQSGGQYHVI 64

Query: 63  IGNHVADVFLAVNSVAGLDEKAQQA-PENDDKGNLLNRFVYVISGIFTPLIGLMAATGIL 121
           IGN V++V+ A+ + +GL    +    E   K N++++    ISG+FTP++  +A  G++
Sbjct: 65  IGNDVSNVYQAMIADSGLSSDVKSGGTEEASKQNVISKLFDFISGVFTPILPAIAGAGMI 124

Query: 122 KGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGAL 181
           KG+LAL LTFQW +++S TY IL +  D  F+F PI+L  +  K+ G N + A  I  A 
Sbjct: 125 KGILALMLTFQWISDKSSTYAILTAIGDGAFYFLPILLAVSVAKKIGTNQYIAAAIAAAA 184

Query: 182 VHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSA 241
           +HP +      G        +FLG+PV  + YSSSVIPI+ + WL S +ER    + P +
Sbjct: 185 LHPQLTALLGAGNT------EFLGLPVVAVVYSSSVIPILLTIWLGSYVERFAEKYSPKS 238

Query: 242 IKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFV 301
           +K    P + L+V+ PV  + VGPL   I   ++ G   L++     AG ++GGF    +
Sbjct: 239 LKIILVPTVTLLVVVPVMLIAVGPLGGIIGSGLSGGIDLLFKHAGLLAGLLIGGFMSPLI 298

Query: 302 MFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAAL 361
           + G+H+ L+P+ INN T+ G+D ++P++  A MAQ GAA GVFL  ++   K +A S ++
Sbjct: 299 ITGMHYALLPIMINNITLNGFDFILPMMFVANMAQAGAAFGVFLRSKNKTFKSLAMSTSI 358

Query: 362 TSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVY----SFGLPSIFTFMQ 417
           T+L GITEPA+YGVN+  K PF+ A I  A G   +   + K Y    S GLP + TF  
Sbjct: 359 TALMGITEPAMYGVNMRLKKPFLAALIGAAAGGVFMSIFKVKSYVISGSAGLPGLPTF-- 416

Query: 418 TIPSTGIDFTVWASVIGGVIAIGCAFVGTVMLHF--ITAKRQPAQGAPQEKTPEVITPPE 475
                 I  T   S+IG VIA   A + T++L F  +  K       P+EK        E
Sbjct: 417 ------IGPTFVYSIIGLVIAFVVATIMTLVLGFKDVPVKDDTKADKPEEKKDTAALQNE 470

Query: 476 QGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIG 535
              + SP+ G++ PL  V D TF++ ++GKG AI+P+VG V +P  G++ ++F T HAIG
Sbjct: 471 V--VQSPLEGQLKPLNQVNDATFSNEIMGKGAAIVPTVGRVVAPFNGKVETIFHTKHAIG 528

Query: 536 IESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPV 595
           ++S+ G E+LIHVGIDTVKLDGK+F++HV  GD +  GD LI FDI  I++ G+D+TTPV
Sbjct: 529 LKSEQGTELLIHVGIDTVKLDGKYFTSHVQSGDLIQAGDVLIDFDIEGIQQEGYDVTTPV 588

Query: 596 LISNSDDFTDVLPHGTAQISAGEPLLSI 623
           +++N++DF  V       I+  E LL++
Sbjct: 589 IVTNTNDFAQVDAKTDGTITVKETLLTV 616


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: 1124
Number of extensions: 65
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: 625
Length of database: 635
Length adjustment: 38
Effective length of query: 587
Effective length of database: 597
Effective search space:   350439
Effective search space used:   350439
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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