GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Phaeobacter inhibens BS107

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF1015 PGA1_c10320 methylcrotonoyl-CoA carboxylase beta chain

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



>FitnessBrowser__Phaeo:GFF1015
          Length = 527

 Score =  701 bits (1810), Expect = 0.0
 Identities = 344/526 (65%), Positives = 402/526 (76%)

Query: 10  PNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTLIDPDSS 69
           P+S  F+ N   H      + E     R GGG + R RHE RGK+  R R+  L+DP S 
Sbjct: 2   PSSEGFKQNREAHLDALGQISEAAETARMGGGEKSRARHESRGKMLPRRRVANLLDPGSP 61

Query: 70  FLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTVKKHLRAQ 129
           FLEIGA AA+ +YD   P AG+V GIGRV G+ VM++ NDATVKGGTYFP+TVKKHLRAQ
Sbjct: 62  FLEIGATAAHAMYDGAAPGAGVVAGIGRVHGQEVMVVCNDATVKGGTYFPMTVKKHLRAQ 121

Query: 130 EIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIACVMGSCT 189
           EIA ENRLPCIYLVDSGGA LP Q EVFPDRDHFGRIFYNQA+MSA+GI QIA VMGSCT
Sbjct: 122 EIAEENRLPCIYLVDSGGANLPQQDEVFPDRDHFGRIFYNQARMSAKGIAQIAVVMGSCT 181

Query: 190 AGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRISGVADYFA 249
           AGGAYVPAMSD  +IVK  GTIFL GPPLVKAATGE V+AE+LGG DVHTR+SGVADY A
Sbjct: 182 AGGAYVPAMSDVTIIVKEQGTIFLAGPPLVKAATGEVVSAEDLGGGDVHTRLSGVADYLA 241

Query: 250 NDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYDVREVIAR 309
            DD  ALA+ R  V  L   +        PE P YDP EI G++P D R  YD+REVIAR
Sbjct: 242 EDDAHALALARRAVQSLNITKPLTVNWASPEEPAYDPEEILGVVPGDLRTPYDIREVIAR 301

Query: 310 IVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIELCCARNIP 369
           +VDGSR  EFK R+G TLV GFAH++G PVGI+ANNG+LFSE+A KGAHF+ELC  R IP
Sbjct: 302 LVDGSRFDEFKPRFGETLVTGFAHVKGCPVGIIANNGVLFSEAAQKGAHFVELCSQRKIP 361

Query: 370 LVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNYGMCGRAY 429
           LVFLQNITGFMVG++YEN GIA+ GAK+VTAV+  NVPK T+++GGSFGAGNYGM GRAY
Sbjct: 362 LVFLQNITGFMVGRKYENEGIARHGAKMVTAVATTNVPKVTMLVGGSFGAGNYGMSGRAY 421

Query: 430 QPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPILAKYEQEG 489
           QPR LW WPN+RISVMGG QAA VL T++RD +  +G   + EE+  F  P +  +E++ 
Sbjct: 422 QPRFLWSWPNSRISVMGGEQAAGVLATVKRDAIERQGGSWSTEEEASFKQPTIDMFEEQS 481

Query: 490 HPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           HP YASARLWDDG+IDP ++R VLAL L+AA  AP++ TRFGVFRM
Sbjct: 482 HPLYASARLWDDGIIDPRKSRDVLALSLSAALNAPIEDTRFGVFRM 527


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: 946
Number of extensions: 37
Number of successful extensions: 2
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: 527
Length adjustment: 35
Effective length of query: 500
Effective length of database: 492
Effective search space:   246000
Effective search space used:   246000
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 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