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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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