GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Methanoculleus horonobensis T10

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_067072575.1 MCUHO_RS01395 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_001602375.1:WP_067072575.1
          Length = 491

 Score =  457 bits (1176), Expect = e-133
 Identities = 228/461 (49%), Positives = 312/461 (67%), Gaps = 4/461 (0%)

Query: 2   FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYL 61
           F K+L+ANRGEIA+RVMRAC ELG+ TVA+YSE D +  HV+YADEA+ +G A  + SYL
Sbjct: 4   FDKILIANRGEIAIRVMRACRELGIDTVAIYSEPDNNALHVKYADEAFCVGEAHPSKSYL 63

Query: 62  DHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARS 121
           + E + + ARK  A+AIHPGYGFLAENA FA+ VE+   T++GPS   +E LG K  ++ 
Sbjct: 64  NKERICDVARKTGAEAIHPGYGFLAENAGFAKLVEEEGLTFIGPSWKTIEALGSKIGSKR 123

Query: 122 LMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQF 181
           +M++A VPV+PGT E   S E+ K VA + GYPV +KA  GGGG G+ +  +E E++   
Sbjct: 124 MMREAGVPVLPGTPEGVTSVEEAKKVAAEIGYPVIVKASAGGGGIGMHIAENEGELEEAI 183

Query: 182 ETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEE 241
           +   R  ++ F + +++VEKYL  PRHIE+Q+LAD  G+  HL +R+CS+QRRHQK++EE
Sbjct: 184 DKGMRIAQSAFGDPTIFVEKYLTKPRHIEIQVLADAKGHTVHLYDRECSIQRRHQKLLEE 243

Query: 242 APSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTEE 301
           AP P ++  LRE++  +A    +AA Y NAGTVEFL  +G +YFMEVNTR+QVEHTVTE 
Sbjct: 244 APCPIMTPALREQMTASAIAAAKAANYKNAGTVEFLYANGNYYFMEVNTRLQVEHTVTEF 303

Query: 302 VTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPG 361
           +TG+D+VK Q+ +AAGE+L   Q+D+ I GH++E RINAE P   FA   G +  Y  PG
Sbjct: 304 ITGIDMVKQQIAIAAGEDLAMGQEDIGIRGHAIECRINAEDPLNNFAADPGKIVRYRSPG 363

Query: 362 GIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPFH 421
           G GIR+D  +  G  I   YDSMI+KL   GSDREE + R  RA+ E+ I G++T +P H
Sbjct: 364 GPGIRVDSGIHMGYTIPAHYDSMISKLCALGSDREEAIQRMRRAIYEYVILGVKTTLPLH 423

Query: 422 RLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVA 462
             ++ +  F  G   T +L E    E I  ++ R+  E  A
Sbjct: 424 YAIMHNAHFIAGDTHTHFLQE----EHIATSLRRYLHEEEA 460


Lambda     K      H
   0.312    0.132    0.371 

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: 670
Number of extensions: 26
Number of successful extensions: 1
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: 601
Length of database: 491
Length adjustment: 35
Effective length of query: 566
Effective length of database: 456
Effective search space:   258096
Effective search space used:   258096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 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