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_017178439.1 A1QA_RS0108255 PTS transporter subunit EIIC

Query= TCDB::ART98499
         (672 letters)



>NCBI__GCF_000295095.1:WP_017178439.1
          Length = 685

 Score =  298 bits (764), Expect = 4e-85
 Identities = 202/678 (29%), Positives = 342/678 (50%), Gaps = 40/678 (5%)

Query: 10  KTIIKDVGGKDNVISVVHCTTRLRFKLKDEKKANDDALKDTDGVVTVV-KAGGQYQVVIG 68
           + I+  VGG DN++ + HC TRLRF+L+D    +   ++   GV+  V ++G +YQ+VIG
Sbjct: 9   EAILDAVGGADNIVHLTHCATRLRFELRDASVIDKATVEAIPGVLGAVPQSGDRYQIVIG 68

Query: 69  NEVADVYEAVLKEGGFSGGGQVADDDLDDSNMS-------LMDKAIDLISGIFTPILGPM 121
             V  +Y  ++          V+D D+  +  S       ++D   + +S  F P+L  +
Sbjct: 69  GAVQGMYTEIMNLPAMKNAAAVSDADVKAAARSKARGKNAIVDAFFEYLSDSFRPLLPVL 128

Query: 122 AAAGMIKGLTAMCASFGWL----AKTSGTYEVLYAIGDGFFYFLPLILAITSAKKFKVDR 177
               +I    A+  +F  +         T     A+    FYF+P+++A  +AKK  +D 
Sbjct: 129 LGTSLIIAGEAVLEAFHIIDTHAENLPPTLVFANAMFQSVFYFMPIMVAYNAAKKLGIDP 188

Query: 178 FTAITIGAAMCYPAMVAMNSSKKVLFDLFNGTFLHSQVHATFLGIPIISMNYTSTVIPII 237
           +    + AA+       ++ S   +    N             G+P+   +Y   V   +
Sbjct: 189 WVGAAVMAALLTQDFAKLSDSASTVCS-HNSLLDKDLCMVHIAGLPMQLNSYGGQVFVPL 247

Query: 238 LAVWFASVVEKWCKEWIPTVVKTFLVPFVTLLIVVPLTFLIIGPLATWIGNALAAITSAV 297
           L V   + + K+  + IP  V+   VPF+  +I++PLT  +IGP+  W+G  + A    +
Sbjct: 248 LMVAILAPLYKYLTKIIPANVQMVFVPFLCFIIMMPLTAFLIGPIGIWLGTGIGAGLFWL 307

Query: 298 YNFSPVLAGILLGGFWQVFVIFGVHWGFVAVMMSNI---AALGYDPILGLSLGASFAQIG 354
           Y+  P +  I +   +   V  G+HW   A+M++NI   A    D I G     +FA  G
Sbjct: 308 YSHVPFVFAIAIPLLYPFLVPLGLHWPLNAIMIANINGDATNHLDYIQGPMGAWNFACFG 367

Query: 355 VVLAILL---QTKDQKLKGIALPAFLSGIFG-VTEPAIYGVTLPRKKPFILSCIAAGVGG 410
              A+L+   + KD +++  +L A  +G+FG ++EP++YG+ L  K+ +    +   VGG
Sbjct: 368 ATAAVLVISVRAKDAEMRQTSLGALAAGLFGGISEPSLYGIHLRFKRIYPFMLVGCFVGG 427

Query: 411 GLIGFFGTKMYMMGGMGVFVIPAAIGPKTGVDMSVYGLMIAMAVSFVLGFILQMALGKKS 470
            +    G  +   GG    V+  A    + + + V+  M   AVS + GF+    L    
Sbjct: 428 LVQAVGG--LLTDGG----VLTGAFAFTSLLTIPVFKPMFLYAVSVLAGFVTSFFLILTF 481

Query: 471 VDQAYDEKQAKAVQ-------------EVASQADAIAKAAPSLASTSDLNVSTELVSPLA 517
             +  +E+ A+A               ++A +A A   AA ++A   +    TE+VSPL 
Sbjct: 482 DYRTKEERAAQAAASGAVEASAEDTAADLALEAGAAGAAAATVAEALEPGAVTEIVSPLT 541

Query: 518 GELLPLSEVKDEVFSSGAMGEGVAVEPS-EGVLHAPADGKVVMTFPTGHAIGMKTSDGAE 576
           G+++ LS+V D VFS+GA+G+G  V PS E V+ APA G VV+   +GHA G+   +G E
Sbjct: 542 GDVMALSDVPDPVFSTGAVGDGAGVTPSGEIVVTAPAAGTVVVAPASGHAYGINLDNGVE 601

Query: 577 ILMHIGMDTVNLQGHGFETLVAKGDEVKAGDELVKFDIDAIHAKGYVVTTPIVVTNSKDY 636
           +L+H+G+DTVNL+G GF+  V +GD V+AG ELV+ D   +   GY +TTP++VTN+  +
Sbjct: 602 LLIHVGIDTVNLEGKGFDVKVKQGDRVEAGQELVRVDRAVVEEAGYSLTTPVLVTNTAKF 661

Query: 637 EKITVVSQGKVKVGQEIL 654
             + + + G V+ G  +L
Sbjct: 662 ASVELAADGGVEQGATLL 679


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: 1084
Number of extensions: 58
Number of successful extensions: 9
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: 685
Length adjustment: 39
Effective length of query: 633
Effective length of database: 646
Effective search space:   408918
Effective search space used:   408918
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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Protein sequences (fasta format)
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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