Alignments for a candidate for bglG in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for bglG in Klebsiella michiganensis M5al

Align PTS beta-glucoside transporter, EIIBCA of 672 aas and 12 predicted TMSs (characterized)
to candidate BWI76_RS07290 BWI76_RS07290 PTS beta-glucoside transporter subunit EIIBCA

Query= TCDB::ART98499
         (672 letters)



>FitnessBrowser__Koxy:BWI76_RS07290
          Length = 626

 Score =  390 bits (1002), Expect = e-112
 Identities = 222/666 (33%), Positives = 362/666 (54%), Gaps = 46/666 (6%)

Query: 4   NYDALAKTIIKDVGGKDNVISVVHCTTRLRFKLKDEKKANDDALKDTDGVVTVVKAGGQY 63
           NY+  A  I+  VGG +N+  + HC TRLR +  D  K ND  +    GV++VV+ GGQ+
Sbjct: 2   NYNETADKILHAVGGAENIRMLTHCATRLRMEFNDRAKVNDAQIGTLPGVISVVEKGGQF 61

Query: 64  QVVIGNEVADVY----EAVLKEGGFSGGGQVADDDLDDSNMSLMDKAIDLISGIFTPILG 119
           Q+VIGNEV  VY    +A+ ++ G +GG      D +     ++ + I +IS  FTP++ 
Sbjct: 62  QIVIGNEVQQVYRRLNKALPEKKGPAGG------DKNAKPAGIVARIISVISTTFTPVIP 115

Query: 120 PMAAAGMIKGLTAMCASFGWLAKTSGTYEVLYAIGDGFFYFLPLILAITSAKKFKVDRFT 179
            +  AGMIK L A+    G +++TS TY++L  I D  F+FLP++LA  ++ KF+ +   
Sbjct: 116 AITGAGMIKALLAILKLTGVISETSSTYQLLNIIADAAFFFLPVLLAYGASLKFECNPIL 175

Query: 180 AITIGAAMCYPAMVAMNSSKKVLFDLFNGTFLHSQVHATFLGIPIISMNYTSTVIPIILA 239
           A+T+   + +P +  M ++ K +                F+GI ++  +Y  +V+PIIL 
Sbjct: 176 AMTLAGVLLHPGIGQMLAAGKAV---------------DFVGINVLLSDYAGSVLPIILT 220

Query: 240 VWFASVVEKWCKEWIPTVVKTFLVPFVTLLIVVPLTFLIIGPLATWIGNALAAITSAVYN 299
           VW  S VE++ ++  P+++K F+ P + LLI  PL  +++GP    + + +AA   A+  
Sbjct: 221 VWLMSWVERFAEKVSPSIIKFFVKPMLILLITAPLALVVVGPAGILLNDLVAAGAGAIDR 280

Query: 300 FSPVLAGILLGGFWQVFVIFGVHWGFVAVMMSNIAALGYDPILGLSLGASFAQIGVV-LA 358
            +  L  +L+G      +I G  W    +    ++  GY+ I G  + AS   +G   L 
Sbjct: 281 HASWLIPMLMGTLQPFLIITGTAWAMTPIATGQLSKSGYEMINGPGMLASNVAMGAATLC 340

Query: 359 ILLQTKDQKLKGIALPAFLSGIFGVTEPAIYGVTLPRKKPFILSCIAAGVGGGLIGFFGT 418
           + L+TK+  L+ +A  +  + + G+TEPA+YGV L  ++  I + I  G  G   G  G 
Sbjct: 341 VALKTKNSNLRQLASSSGFTALLGITEPALYGVLLKFRRVLIAAMIGGGCAGVYAGVSGL 400

Query: 419 KMYMMGGMGVFVIPAAIGPKTGVDMSVYGLMIAMAVSFVLGFILQMALGKKSVDQAYDEK 478
             Y     G+  +PA IG      M++   ++  A+S V+ F L   +  K V +  +E 
Sbjct: 401 VRYAFVSPGLAALPAFIGENP---MNIVHALVTCAISIVVTFTLTWFIAFKDVPEEQEE- 456

Query: 479 QAKAVQEVASQADAIAKAAPSLASTSDLNVSTELVSPLAGELLPLSEVKDEVFSSGAMGE 538
                             AP  A +      TE+ SPL G+++ LSEV D+VFS G +GE
Sbjct: 457 ---------------VGEAPQPAVSPKNEGETEVFSPLRGQVVALSEVNDDVFSGGLLGE 501

Query: 539 GVAVEPSEGVLHAPADGKVVMTFPTGHAIGMKTSDGAEILMHIGMDTVNLQGHGFETLVA 598
           G+A+ P EGVL AP  G V+M  P+ HA+G+++  G E+L+HIG+DTVNL G  F + + 
Sbjct: 502 GLAIRPEEGVLRAPFSGTVMMFLPSCHAVGLQSDSGLELLIHIGIDTVNLNGQHFSSTLK 561

Query: 599 KGDEVKAGDELVKFDIDAIHAKGYVVTTPIVVTNSKDYEKITVVSQGKVKVGQEILDLEG 658
            GD V+AG EL++FDI AI   GY + TP++V N  +   + + +  +V  G++++ ++ 
Sbjct: 562 VGDRVEAGQELIRFDIPAIEQAGYDLITPVIVVNGDEQHSLRLTAAAQVDYGEQLM-VQS 620

Query: 659 ASETEA 664
           A E +A
Sbjct: 621 AKEAQA 626


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: 1014
Number of extensions: 49
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: 626
Length adjustment: 38
Effective length of query: 634
Effective length of database: 588
Effective search space:   372792
Effective search space used:   372792
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 17 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 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