Alignments for a candidate for liuD in Flavobacterium ummariense DS-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuD in Flavobacterium ummariense DS-12

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_091525366.1 BM253_RS13550 methylcrotonoyl-CoA carboxylase

Query= BRENDA::Q9LDD8
         (587 letters)



>NCBI__GCF_900115115.1:WP_091525366.1
          Length = 547

 Score =  496 bits (1277), Expect = e-144
 Identities = 263/539 (48%), Positives = 348/539 (64%), Gaps = 27/539 (5%)

Query: 61  FSSNSIAMEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELS 120
           F+ N    + +LSEL+  + KV  GGGE+ + +   + K+  RERID L D  S  +E+ 
Sbjct: 5   FNKNEDHNKLLLSELKQKLAKVKLGGGEKRIAKLHEQGKMTARERIDFLFDKDSKSIEIG 64

Query: 121 QLAGHELYEEP--LPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIA 178
              G  +Y+E    PSGG++  IG ++G+  + +AND TVK G ++PIT KK+LRAQEIA
Sbjct: 65  AFVGEGMYKEHGGCPSGGVVVKIGYVNGKQVIVVANDATVKAGAWFPITGKKNLRAQEIA 124

Query: 179 ARCRLPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGG 238
            + RLP IYLVDS G YLP Q E+FPDKENFGR+F N ++MSS GI QIA V+GSC AGG
Sbjct: 125 IKNRLPIIYLVDSAGVYLPMQDEIFPDKENFGRIFRNNAIMSSMGITQIAAVMGSCVAGG 184

Query: 239 AYIPAMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDE 298
           AY+P M+DE+++V   G+IFLAG  LVKAA GE +  E LGGAT H  +SGV+DY A+D+
Sbjct: 185 AYLPIMSDEALIVDKTGSIFLAGSYLVKAAIGESIDNETLGGATTHTEISGVTDYKAKDD 244

Query: 299 LHGLAIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINELRSIAPVDHKQQFDVRSI 358
              L   RNIV       K G     G   +  K+P  D NE+  I P    +Q+D   I
Sbjct: 245 KDCLETIRNIV------GKMGDFDKAGYNRIDTKKPALDPNEIYGILPKSRGEQYDTMEI 298

Query: 359 IARIVDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGN-------------------NGI 399
           I R+VD SEFDE+K  YG T++TG+ARI G  VGI+ N                    G+
Sbjct: 299 IKRLVDDSEFDEYKAGYGQTIITGYARIDGWAVGIVANQRKVVKTTGAKTKPSEMQFGGV 358

Query: 400 LFNESALKGAHFIELCSQRKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVP 459
           ++++SA K   FI  C+Q+KIPLVFLQ++TGFMVGS++E  GI K GAKMV AVS + VP
Sbjct: 359 IYSDSADKATRFIANCNQKKIPLVFLQDVTGFMVGSKSEHGGIIKDGAKMVNAVSNSVVP 418

Query: 460 KITIITGASFGAGNYAMCGRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGI 519
           K T+I G S+GAGNYAMCG+AY P F   WP+A + +MGGAQAA VL QIE ++ K +G 
Sbjct: 419 KFTVIMGNSYGAGNYAMCGKAYDPRFFLAWPSAELAVMGGAQAAKVLLQIEASSLKAKGE 478

Query: 520 KWTEEEEEAFKKKTVDAYEREANPYYSTARLWDDGVIDPCDTRKVLGLCLSAALNRPLE 578
           + T E+E     K    Y+ + +PYY+ ARLW D +IDP DTRK + + + AA + P+E
Sbjct: 479 ELTPEKEAELFDKIKAKYDAQTSPYYAAARLWTDAIIDPLDTRKWISMGIEAANHAPIE 537


Lambda     K      H
   0.320    0.138    0.408 

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: 818
Number of extensions: 51
Number of successful extensions: 4
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: 587
Length of database: 547
Length adjustment: 36
Effective length of query: 551
Effective length of database: 511
Effective search space:   281561
Effective search space used:   281561
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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