Alignments for a candidate for liuD in Coprobacter fastidiosus NSB1

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuD in Coprobacter fastidiosus NSB1

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_022601414.1 NSB1T_RS23465 acyl-CoA carboxylase subunit beta

Query= BRENDA::Q9LDD8
         (587 letters)



>NCBI__GCF_000473955.1:WP_022601414.1
          Length = 517

 Score =  248 bits (633), Expect = 4e-70
 Identities = 165/509 (32%), Positives = 247/509 (48%), Gaps = 44/509 (8%)

Query: 72  LSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE----- 126
           + EL +  ++   GGGE  ++    + K   RERI  LLD GS F E+     H      
Sbjct: 8   VKELIALREQARLGGGERRIESQHKKGKYTARERISMLLDEGS-FEEIDMFVRHRSVNFG 66

Query: 127 LYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCRLPCI 186
           + +E     G++TG G I GR+    A D TV GG+       K  +  + A +   P I
Sbjct: 67  IDKESYLGDGVVTGTGTIAGRLVYVFAQDFTVFGGSLSETFAMKICKIMDQAMKMGAPVI 126

Query: 187 YLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIPAMAD 246
            + DSGGA + +          +  +F   ++++S  IPQI+ + G C  G  Y PA+ D
Sbjct: 127 GINDSGGARIQEGVNALA---GYAEIF-QRNILASGVIPQISGIFGPCAGGSVYSPALTD 182

Query: 247 ESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGLAIGR 306
            ++M +G   +FL GP +VK  TGE+V+ E LGGA+VH T SGV+ +    E  GL + R
Sbjct: 183 FNIMTRGTSYMFLTGPKVVKTVTGEDVTQEQLGGASVHATKSGVAHFAVDTEEDGLKLIR 242

Query: 307 NIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINE--------LRSIAPVDHKQQFDVRSI 358
           +++             +F  +N + + PL D  +        L  I P +  + +D+  +
Sbjct: 243 HLM-------------SFLPQNNMEEPPLVDCEDPIDRLEDSLNDIIPDEPNRAYDMYEV 289

Query: 359 IARIVDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIE 413
           I  I+D  EF E  K Y   ++ GFAR  GQ+VGII N      G+L   ++ K A F+ 
Sbjct: 290 IGAIIDNGEFLEVHKDYAQNIIVGFARFNGQSVGIIANQPNKMAGVLDINASRKAARFVR 349

Query: 414 LCSQRKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGN 473
            C    IPLV L ++ GF+ G+  E  G+   GAK++ A   A VPK+T+    S+G   
Sbjct: 350 FCDAFNIPLVTLVDVPGFLPGTGQEYGGVILHGAKLLYAYGEATVPKVTVTLRKSYGGAY 409

Query: 474 YAMCGRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKT 533
             M  +    D  + WP A I +MG + A  V+   E A  +      T  E+EA  KK 
Sbjct: 410 CVMSSKHLRGDVNYAWPTAEIAVMGPSGAVEVIFAKEVAASENPAA--TAAEKEAEYKKV 467

Query: 534 VDAYEREANPYYSTARLWDDGVIDPCDTR 562
                  ANPY +    + D VI+P +TR
Sbjct: 468 F------ANPYNAARYGYIDDVIEPRNTR 490


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: 742
Number of extensions: 42
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: 587
Length of database: 517
Length adjustment: 36
Effective length of query: 551
Effective length of database: 481
Effective search space:   265031
Effective search space used:   265031
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.

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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