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 β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_051000578.1 A1QA_RS14145 PTS beta-glucoside transporter subunit IIBCA

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000295095.1:WP_051000578.1
          Length = 675

 Score =  343 bits (879), Expect = 2e-98
 Identities = 224/674 (33%), Positives = 347/674 (51%), Gaps = 63/674 (9%)

Query: 4   LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63
           +A  ++  VGGA+NI +  HCATRLR  L D  K   + L K P I     +GG +Q+++
Sbjct: 8   VATDVLTYVGGAENITAAAHCATRLRLVLADLDKVDQKALDKDPDIKGTFIAGGMYQIIV 67

Query: 64  G----NHVADVFLAVNSVAGL--DEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAA 117
           G    + V D  +A   V  +  DE  Q A ++   GNL++RF+ +I+ IF P++  + A
Sbjct: 68  GPGDVDQVFDRMIATGGVKEVSKDEAKQVAAQS---GNLVSRFIKMIADIFVPILPALIA 124

Query: 118 TGIL---------KGMLA-LALTFQWTTEQSGTYLILFSA-SDALFWFFPIILGYTAGKR 166
            G++         +G+   ++L  +WT    G Y  L +  S A F F P+++G++A KR
Sbjct: 125 GGLMMAINNVLTAEGLFGDMSLKERWTW--LGDYADLINLISSAAFAFLPVLVGFSAAKR 182

Query: 167 FGGNPFTAMVIGGALVHPLILTAFENGQ-KADALGLDF---------LGIPVTLLNYSSS 216
           FGGN +    +G A+V   +L+A++  + +A A   +F          G+ V  + Y + 
Sbjct: 183 FGGNVYLGGAMGAAMVSSSLLSAYDMSKPEAAAKFWEFTGAASSWHLFGLEVQKIGYQAM 242

Query: 217 VIPIIFSAWLCSILERRLNAWLPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAA 276
           VIPII  A+L S++E+RL+  L        TPL+ L+    +TF+++GP++  +S  I  
Sbjct: 243 VIPIICVAYLMSVIEKRLHKRLSGTADFLLTPLITLLGTGFLTFVVIGPITRQLSIWITD 302

Query: 277 GYLWLYQAVPAFAGAVMGGFWQIFVMFGLHWGL----VPLCINNFTVLGYDTMIPLLMPA 332
           G  W Y  +    GA+ G  +   V+ GLH       +PL I++    G   + P+   A
Sbjct: 303 GLDWTYNTLGPLGGALFGLVYSPIVVTGLHQSFPAVEIPL-ISDIANTGGSFIFPIASMA 361

Query: 333 IMAQVGAALGVFLCERDAQKKVVAGSAALTSLFGITEPAVYGVNLPRKYPFVIACISGAL 392
            +AQ   A+ VF   RDA+ K +AG+  +++L GITEPA++GVNL  ++PF I   S A+
Sbjct: 362 NVAQGAVAIAVFFRARDAKMKGLAGAGGVSALLGITEPAIFGVNLRLRWPFFIGMGSAAI 421

Query: 393 GATIIGYAQTKVYSFGLPSIFTFMQTIPS-----TGIDFTVWASVIGGVIAIGCAFVGTV 447
           GA ++     +  + G      F+  +P        ++  V A    G         G  
Sbjct: 422 GAALVAVFNVRSQALGAAGFVGFVSMVPKHIPAYLALEVLVAAIAFSGAYFYSRTAKGAA 481

Query: 448 ML------------------HFITAKRQPAQGAPQEKTPEVITPPEQGGICSPMTGEIVP 489
            L                  H  TA+  P +    E   E     E   + SP+ G +VP
Sbjct: 482 SLADGDVEDEAALEAEAEAAHEHTAEDAPHEAVKAELPAEAA---EDYSVTSPIEGRVVP 538

Query: 490 LIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIESDDGVEILIHVG 549
           L  V D  F+ GLLG G+A++PS G V SPV G +   F + HA GI +  GVEILIHVG
Sbjct: 539 LSEVEDAVFSQGLLGPGLAVVPSTGPVVSPVDGEVIVAFPSGHAYGIRAASGVEILIHVG 598

Query: 550 IDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLISNSDDFTDVLPH 609
           +DTV+LDGK FS  V+ GD +  G  L+  D  A+++AG+ + TP+++SN D F+ +   
Sbjct: 599 MDTVQLDGKHFSPKVHQGDVIRRGTPLVEVDWDAVKKAGYQIVTPIVVSNGDKFSGISEA 658

Query: 610 GTAQISAGEPLLSI 623
           GT   S G+ L S+
Sbjct: 659 GTRDASRGDALFSV 672


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: 1189
Number of extensions: 64
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: 675
Length adjustment: 38
Effective length of query: 587
Effective length of database: 637
Effective search space:   373919
Effective search space used:   373919
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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Candidates (tab-delimited)
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