GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Rhodobacter ovatus JA234

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_097030693.1 CRO07_RS10730 methylcrotonoyl-CoA carboxylase

Query= metacyc::MONOMER-17283
         (535 letters)



>NCBI__GCF_900207575.1:WP_097030693.1
          Length = 534

 Score =  686 bits (1770), Expect = 0.0
 Identities = 333/530 (62%), Positives = 403/530 (76%)

Query: 6   SHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLID 65
           S + P+S  F+ N   H +L AD+         GGG   + RH  RGKL  R+R+  L+D
Sbjct: 5   SRVLPSSESFRRNREAHLALIADIARAADLAAAGGGPAAQARHAARGKLPPRERVAGLLD 64

Query: 66  PDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKH 125
           P S FLEIGA AA+ +YD   PAAG++ GIGRV G  VM++ NDATVKGGTY+P+TVKKH
Sbjct: 65  PGSPFLEIGAFAAHGMYDGAAPAAGVIAGIGRVHGAEVMVVCNDATVKGGTYYPMTVKKH 124

Query: 126 LRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVM 185
           LRAQEIA E RLPC+YLVDSGGA LP Q EVFPDRDHFGRIF+NQA+MSA GIPQIA VM
Sbjct: 125 LRAQEIAAECRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFFNQARMSAAGIPQIAVVM 184

Query: 186 GSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVA 245
           GSCTAGGAYVPAMSD  +IV+  GTIFL GPPLV+AATGE V+AE+LGG DVHTR+SGVA
Sbjct: 185 GSCTAGGAYVPAMSDVTIIVRDQGTIFLAGPPLVRAATGEVVSAEDLGGGDVHTRLSGVA 244

Query: 246 DYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVRE 305
           DY A DD  AL + R  + +L   + A  + + PE P +DP +I G++P D R  +D+RE
Sbjct: 245 DYLAEDDAHALILARRALGNLNRTRPATVQWQSPEDPAHDPEDILGLVPADLRTPWDIRE 304

Query: 306 VIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELCCA 365
           +IARI DGSR  EFK R+G TLV GFAH+ G PVGI+ANNG+LFSE+A+KGAHFIELC  
Sbjct: 305 LIARITDGSRFDEFKPRFGETLVTGFAHLMGCPVGIVANNGVLFSEAAIKGAHFIELCSQ 364

Query: 366 RNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMC 425
           R IPL+FLQNITGFMVG++YEN GIA+ GAK+VTAV+   VPK T+++GGSFGAGNYGM 
Sbjct: 365 RAIPLIFLQNITGFMVGRKYENEGIARHGAKMVTAVATTAVPKITMLVGGSFGAGNYGMA 424

Query: 426 GRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKY 485
           GRAY PR LW WPN+RISVMGG QAA VL T+R D L   G   TPE++  F  P +  +
Sbjct: 425 GRAYSPRFLWTWPNSRISVMGGEQAAGVLATVRGDALARAGTPWTPEDEAAFKRPTIEMF 484

Query: 486 EQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           +++ HP YASARLWDDG++DP +TR  LAL L+AA  AP++PTRFG+FRM
Sbjct: 485 DRQSHPLYASARLWDDGIVDPRKTRETLALSLSAALNAPIEPTRFGLFRM 534


Lambda     K      H
   0.322    0.139    0.423 

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: 924
Number of extensions: 34
Number of successful extensions: 3
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: 535
Length of database: 534
Length adjustment: 35
Effective length of query: 500
Effective length of database: 499
Effective search space:   249500
Effective search space used:   249500
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 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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