Alignments for a candidate for liuB in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Thiothrix lacustris DSM 21227

Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA carboxylase biotin-containing subunit; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate WP_245606761.1 Q394_RS0109245 pyruvate carboxylase

Query= SwissProt::Q96RQ3
         (725 letters)



>NCBI__GCF_000621325.1:WP_245606761.1
          Length = 1169

 Score =  377 bits (968), Expect = e-108
 Identities = 199/454 (43%), Positives = 281/454 (61%), Gaps = 9/454 (1%)

Query: 47  RNITKVLIANRGEIACRVMRTAKKLGVQTVAVYSEADRNSMHVDMADEAYSIGPAPSQ-Q 105
           R I K+L+ANRGEIA R++R A +L ++TV+VY+  DR S H   ADEAY IG      +
Sbjct: 25  RPINKLLVANRGEIAIRILRAASELKLRTVSVYTYEDRFSPHRYKADEAYQIGKDDEPLK 84

Query: 106 SYLSMEKIIQVAKTSAAQAIHPGCGFLSENMEFAELCKQEGIIFIGPPPSAIRDMGIKST 165
            YL +E II+VAK +   AIHPG GFLSEN+ FA  C++EGIIFIGP P A++ +G K  
Sbjct: 85  PYLDIEAIIKVAKRNHVDAIHPGYGFLSENVTFARRCREEGIIFIGPTPEAMQKLGDKVA 144

Query: 166 SKSIMAAAGVPVVEGYHGEDQSDQCLKEHARRIGYPVMIKAVRGGGGKGMRIVRSEQEFQ 225
           +K I  A+G+PV+E       + +  K  A RIGYP+M+KA  GGGG+GMR++R   + +
Sbjct: 145 AKEIAIASGLPVIEDSREPLDTLEIAKREADRIGYPLMMKAASGGGGRGMRVLREPSQLE 204

Query: 226 EQLESARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKI 285
                AR EA K+F D  + +EK++D+P+H+E+Q+ GD HGN V+L+ERDCSVQRR QK+
Sbjct: 205 GAYNDARNEALKAFGDATVFLEKYIDSPKHIEIQILGDTHGNIVHLYERDCSVQRRFQKV 264

Query: 286 IEEAPAPGIKSEVRKKLGEAAVRAAKAVNYVGAGTVEFIMDSKHNFCFMEMNTRLQVEHP 345
           +E AP+ G+K E R+ L + A+   + V+Y  AGTVEF++D      F+E+N R+QVEH 
Sbjct: 265 VEVAPSTGLKDETRENLYKYALAITRHVDYSCAGTVEFLVDKDERIYFIEVNPRVQVEHT 324

Query: 346 VTEMITGTDLVEWQLRIAAGEKIP------LSQEEITLQGHAFEARIYAEDPSNNFMPVA 399
           +TE ITG D+V  Q+ IA G K+        SQE +   G+A + RI  EDP N F P  
Sbjct: 325 ITEEITGIDIVRSQILIAGGAKLDDPEIGIPSQESVECNGYAVQCRITTEDPENGFKPDY 384

Query: 400 GPLVHLSTPRADPSTRIETGVR-QGDEVSVHYDPMIAKLVVWAADRQAALTKLRYSLRQY 458
           G ++   +       R++ G    G +VS  +D M+ K+  W    + A  +   +L+++
Sbjct: 385 GTIIAYRS-SGGFGVRLDAGAAYPGAKVSPFFDSMLVKVTTWGRSLEGASNRNLRALQEF 443

Query: 459 NIVGLHTNIDFLLNLSGHPEFEAGNVHTDFIPQH 492
            I G+ TNI FL N+  HP F  G     FI  H
Sbjct: 444 RIRGVKTNIGFLENVLQHPVFTTGKCTVTFIDNH 477



 Score = 49.3 bits (116), Expect = 1e-09
 Identities = 27/63 (42%), Positives = 36/63 (57%)

Query: 653  MTGTIEKVFVKAGDKVKAGDSLMVMIAMKMEHTIKSPKDGTVKKVFYREGAQANRHTPLV 712
            + G +  V VKAGD+V+    L V+ AMKME TI +P  G VKKV    G    +   ++
Sbjct: 1107 LQGKLSTVMVKAGDEVEENTPLFVIEAMKMETTITAPAAGKVKKVHLPAGELVEQGDLVI 1166

Query: 713  EFE 715
            EFE
Sbjct: 1167 EFE 1169


Lambda     K      H
   0.317    0.131    0.377 

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: 1617
Number of extensions: 58
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 2
Length of query: 725
Length of database: 1169
Length adjustment: 43
Effective length of query: 682
Effective length of database: 1126
Effective search space:   767932
Effective search space used:   767932
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
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