Alignments for a candidate for pccA1 in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA1 in Sinorhizobium meliloti 1021

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate SM_b21124 SM_b21124 methylcrotonoyl-CoA carboxylase biotinylated subunit

Query= metacyc::MONOMER-13597
         (509 letters)



>FitnessBrowser__Smeli:SM_b21124
          Length = 662

 Score =  363 bits (932), Expect = e-104
 Identities = 205/500 (41%), Positives = 291/500 (58%), Gaps = 19/500 (3%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           FS++L+ANRGEIA R+++  + +G+  +AVYS+AD  A+H   ADEA  IG APA +SYL
Sbjct: 2   FSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
               I+ AA      AIHPGYGFLSENA+FAEAV +AG+ F+GP    +R +  K   K 
Sbjct: 62  ASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAKA 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           L   +GVP  PG  G           A +IGYP+++KA +GGGG G+ RV+ Q+      
Sbjct: 122 LMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPAL 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
           E  +R A  AFG   + +E+Y   PRHIE Q+ GD++GN V  +ER+C++QRR+QK+IEE
Sbjct: 182 EAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSR-----DFYFLELNKRLQV 298
           AP+P +  E R +M +  ++  + I Y   GT E   +DV+       FYF+E+N RLQV
Sbjct: 242 APAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVE-FIADVTNGLWPDHFYFMEMNTRLQV 300

Query: 299 EHPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSG 358
           EHP TE I  IDLV+ Q+++A+GE LP  Q D++  + G A E R+ AED    F  ++G
Sbjct: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADIS--MNGWAFEARLYAEDPARGFLPATG 358

Query: 359 FVTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIG 418
            +T    P G   RVDSG+  G  + PYYD L++KLIV+G++R  A+     AL + +IG
Sbjct: 359 RLTELSFPEGTS-RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIG 417

Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLLR 478
           G  T  +    + ++ DF+ G   T  I           RE E + A +A   ++  L  
Sbjct: 418 GTVTNRDFLIRLTEEHDFRSGHPDTGLID----------REIERLTAPVAPGDEALALAA 467

Query: 479 TSSTDNKGKAQSKSGWKTYG 498
             ST      +S   W + G
Sbjct: 468 IFSTGALDPNRSTDPWSSLG 487


Lambda     K      H
   0.317    0.135    0.385 

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: 782
Number of extensions: 43
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: 509
Length of database: 662
Length adjustment: 36
Effective length of query: 473
Effective length of database: 626
Effective search space:   296098
Effective search space used:   296098
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 (21.6 bits)
S2: 53 (25.0 bits)

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

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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