Alignments for a candidate for bglG in Actinomyces timonensis 7400942

GapMind for catabolism of small carbon sources

Alignments for a candidate for bglG in Actinomyces timonensis 7400942

Align PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs (characterized)
to candidate WP_026048827.1 A1QA_RS0108840 PTS transporter subunit EIIC

Query= TCDB::ART98499
         (672 letters)



>NCBI__GCF_000295095.1:WP_026048827.1
          Length = 637

 Score =  492 bits (1267), Expect = e-143
 Identities = 278/669 (41%), Positives = 395/669 (59%), Gaps = 45/669 (6%)

Query: 1   MAK-NYDALAKTIIKDVGGKDNVISVVHCTTRLRFKLKDEKKANDDALKDTDGVVTVVKA 59
           MAK +Y A+A  +++ +GG+ N+ ++ HC TR+RF LKDE KA+  A+KD  GVVTVV+ 
Sbjct: 1   MAKVDYAAMAPDLLQRIGGEANISALSHCATRMRFVLKDESKADSAAIKDMAGVVTVVQT 60

Query: 60  GGQYQVVIGNEV----ADVYEAVLKEGGFSGGGQVADDDLDDSNMSLMDKAIDLISGIFT 115
           GGQYQVVIGN+V    A++   +   G   G G+        ++ + +D  I L+S IF 
Sbjct: 61  GGQYQVVIGNDVPLLFAEMQALLPGLGSEKGEGEKGGA----ASRNPLDAFIALVSAIFL 116

Query: 116 PILGPMAAAGMIKGLTAMCASFGWLAKTSGTYEVLYAIGDGFFYFLPLILAITSAKKFKV 175
           P+L  +A  G+ K   AM A+F W+ K S TY VL A  D F  FLPL+LA+T+A+ FK 
Sbjct: 117 PVLWTLAGTGLFKAFLAMFATFNWIDKASDTYTVLNAAADAFMNFLPLVLAVTAARHFKA 176

Query: 176 DRFTAITIGAAMCYPAMVAMNSSKKVLFDLFNGTFLHSQVHATFLGIPIISMNYTSTVIP 235
           ++FTA+ I  A+ YP+++AMN               HS     FLGIP++ M+YTS+V+P
Sbjct: 177 NQFTAMAIAGALVYPSIIAMNDGGS-----------HS-----FLGIPLVIMSYTSSVLP 220

Query: 236 IILAVWFASVVEKWCKEWIPTVVKTFLVPFVTLLIVVPLTFLIIGPLATWIGNALAAITS 295
           II+AVW  S +E+ C    P+  + F+ P++T+LI+VPLT L IGPL T + + +A+   
Sbjct: 221 IIVAVWVQSYIERVCNRVFPSAFRNFMTPWITVLIMVPLTLLTIGPLTTTVADGIASGVQ 280

Query: 296 AVYNFSPVLAGILLGGFWQVFVIFGVHWGFVAVMMSNIAALGYDPILGLSLGASFAQIGV 355
            ++   P+L GI++GGFWQVFV+FG+HWG V +M   I   GY  I G    A  AQ   
Sbjct: 281 WLFVHVPLLGGIVIGGFWQVFVMFGLHWGLVPIMTQEITTNGYSLIYGPIEAAVLAQAAA 340

Query: 356 VLAILLQTKDQKLKGIALPAFLSG-IFGVTEPAIYGVTLPRKKPFILSCIAAGVGGGLIG 414
            LA++L+++D K++ +A PA LSG + GVTEP IYG+ LPRK PF    +   VGG +  
Sbjct: 341 GLAVMLRSRDAKVRELAGPASLSGFLAGVTEPIIYGINLPRKLPFYFGILGGAVGGAIGA 400

Query: 415 FFGTKMYMMGGMGVFVIPAAIGPKTGVDMSVYGL-MIAMAVSFVLGFILQMALGKKSVDQ 473
             G ++   G     V P+ IG    ++   + + +I + V  ++ F L    G K    
Sbjct: 401 LAGGRVSQAG-----VFPSLIGLPAYLETPHFVVWLIGVIVGVIIAFTLTFMFGVKD--- 452

Query: 474 AYDEKQAKAVQEVASQADAIAKA-----APSLASTSDLNVSTELVSPLAGELLPLSEVKD 528
                 A A  E A  A   AKA     A S  + +D   +T LV+P+ G  LPL  VKD
Sbjct: 453 -----DAVAAGEQAGSAAGAAKAAGAAGAGSSTAVADAEPTTALVAPVDGRALPLERVKD 507

Query: 529 EVFSSGAMGEGVAVEPSEGVLHAPADGKVVMTFPTGHAIGMKTSDGAEILMHIGMDTVNL 588
            VFSSGA+G GV + PS G L APA G ++    TGHA G+K  DG EIL+H+G+DTVNL
Sbjct: 508 PVFSSGALGNGVGIVPSAGGLAAPAAGTIITAMETGHAFGIKADDGVEILIHVGIDTVNL 567

Query: 589 QGHGFETLVAKGDEVKAGDELVKFDIDAIHAKGYVVTTPIVVTNSKDYEKITVVSQGKVK 648
           +G GF   VA GD V  GD LV  D+ A+   GY  TT +VVTN+     +  +  G+V+
Sbjct: 568 KGAGFTPRVAVGDRVSIGDPLVDVDLAAVRDAGYDTTTIVVVTNTASLGAVVPIIDGEVR 627

Query: 649 VGQEILDLE 657
            G+ I++++
Sbjct: 628 AGETIVEID 636


Lambda     K      H
   0.321    0.137    0.398 

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: 1214
Number of extensions: 79
Number of successful extensions: 5
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: 672
Length of database: 637
Length adjustment: 38
Effective length of query: 634
Effective length of database: 599
Effective search space:   379766
Effective search space used:   379766
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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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