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

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_034281422.1 BA81_RS07770 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000691165.1:WP_034281422.1
          Length = 619

 Score =  334 bits (856), Expect = 8e-96
 Identities = 208/612 (33%), Positives = 316/612 (51%), Gaps = 30/612 (4%)

Query: 2   TELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQV 61
           T++A+ ++  +GG +NI  L HC+TRLRF L D+ KA    L+KTPG+I  V   GQ QV
Sbjct: 4   TQVAKDVLQHIGGKENIAHLEHCSTRLRFTLIDQKKADVPALEKTPGVI-AVRMSGQCQV 62

Query: 62  VIGNHVADVFLAVNSVAGLDEKAQQAPENDDK-----GNLLNRFVYVISGIFTPLIGLMA 116
           VIGN V +V+  V S+ G    +Q  P N  K     G +L  F+    G+F PL+  +A
Sbjct: 63  VIGNDVIEVYQKVTSLIGSSSSSQDVPSNQPKEKRKAGTVLLDFIV---GVFQPLVPAIA 119

Query: 117 ATGILKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMV 176
             GILK  L L     W   +  TY IL    DA  +F P+++  T   +   NP  A+ 
Sbjct: 120 GGGILKSFLLLFSLLGWMDAKGQTYQILNMVGDAPLYFLPLLVAVTTANKLKVNPLVALS 179

Query: 177 IGGALVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNA 236
             GAL+ P +      G +        L   V  + Y+  V P I S  L + +E+    
Sbjct: 180 AVGALLLPNMTAMLTEGAQ-------LLSFDVKNIAYAYQVFPAILSVLLYAQMEKFFTR 232

Query: 237 WLPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGF 296
           + P  I+ FF P++ L++  PVT LL+GP+     +  ++  L ++  V   A A++   
Sbjct: 233 FSPKPIRIFFVPMMSLVITVPVTLLLLGPIGFTAGQGFSSIILAMFNTVGWVAVAILAAV 292

Query: 297 WQIFVMFGLHWGLVPLCINNFTVLGYDTM-IPLLMPAIMAQVGAALGVFLCERDAQKKVV 355
               V  G+H  +VP  +     LG + + +P  +   +A+ GA   V L  +D   +  
Sbjct: 293 LPFMVASGMHKAMVPYAVTTMGTLGKEALYLPASLAHNIAESGACFAVALRTKDKVLRST 352

Query: 356 AGSAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTF 415
           A SA +++ FGITEPA+YGV L  K       I   +G   IG    + +    P + + 
Sbjct: 353 AISAGISAFFGITEPALYGVTLQNKRVLGSVMIGSFVGGIFIGLVGIQAFVLVGPGLASM 412

Query: 416 MQTIPSTGIDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITPPE 475
              I S  +   +  ++IG VI+   AF+      F+  K +  +    EKT +     E
Sbjct: 413 SMFI-SDELPRNLMFAIIGAVISFIVAFIAA----FVLGKDRTVE----EKTKDQAAFAE 463

Query: 476 QGG----ICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATL 531
           Q G      SP+ G+++ L  V D  F+S ++G GIAI+PS G + +PV G +  LF T 
Sbjct: 464 QIGAGETFKSPVIGQMISLSEVKDDIFSSKVMGDGIAIVPSKGALYAPVDGEVTLLFETN 523

Query: 532 HAIGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDL 591
           HA+G+++D GVE+L H+GIDTV+L+G++F   V  GD+V  GD LI FD+  I EAG+D 
Sbjct: 524 HALGMKTDQGVEVLFHIGIDTVQLEGQYFYPKVQAGDRVQAGDLLIEFDLEKIMEAGYDP 583

Query: 592 TTPVLISNSDDF 603
            T  +I+N+D +
Sbjct: 584 VTLAVITNTDQY 595


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: 1001
Number of extensions: 60
Number of successful extensions: 7
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: 619
Length adjustment: 37
Effective length of query: 588
Effective length of database: 582
Effective search space:   342216
Effective search space used:   342216
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.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources