GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Pseudomonas fluorescens FW300-N2C3

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 AO356_07595 AO356_07595 acetyl-CoA carboxylase biotin carboxylase subunit

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_07595
          Length = 457

 Score =  376 bits (966), Expect = e-109
 Identities = 188/439 (42%), Positives = 287/439 (65%), Gaps = 5/439 (1%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           ++LVANRGEIA R+++A KE+G+  +A  SEAD  +   + ADE + +G A A  SYLN+
Sbjct: 7   KLLVANRGEIAVRIIRAAKELGIPTVAACSEADVDSQAARMADEVHILGPARADKSYLNV 66

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
           E ++ A +    +A+HPGYGFLSENA+FAEAV  AG  F+GPS+E +R++ DK + +R A
Sbjct: 67  EALLGALKATGANAVHPGYGFLSENADFAEAVVAAGAIFVGPSAETIRRMGDKAEARRTA 126

Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185
             AGVP  PGS G +  ++ AL+ A+ +G+P+++KA++GGGG GI   +N +QL + + R
Sbjct: 127 QAAGVPVVPGSPGELFDVESALQAAQSVGFPLLIKASAGGGGRGIRLAENAEQLSEEFPR 186

Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVV-AWERECTIQRRNQKLIEEA 244
           ++R A  AFG   +++E++    RHIE Q++GD  G + V  +EREC++QRR QK+ EEA
Sbjct: 187 SQREAQAAFGNGAVYLERFISRARHIEVQVLGD--GQHAVHLFERECSLQRRRQKIFEEA 244

Query: 245 PSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTE 304
           PSP L  ++R+++ E  ++  + + Y   GT E  + D + +F+F+E+N R+QVEHP +E
Sbjct: 245 PSPVLSQQQRKTLCESAVRLTESLGYKGAGTLEYLYDDATGEFFFIEMNTRIQVEHPVSE 304

Query: 305 LIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYR 364
           LI  IDLV+  +++A GE L F Q D+  R+ G A++ R+NAED   +F  S G V    
Sbjct: 305 LITGIDLVQSMLRIAGGEPLGFKQSDI--RLNGAALQMRLNAEDPARDFFPSPGLVEELI 362

Query: 365 EPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTI 424
            P G G+RVD+ +  G  VPPYYDSL++KLI++G  R  A+     A+A   + G+  T+
Sbjct: 363 WPNGAGIRVDTHLYQGYRVPPYYDSLLAKLIIHGADRAEALARARMAVAHTTLTGMANTL 422

Query: 425 ELYKWIMQDPDFQEGKFST 443
            L+  +++ P      F T
Sbjct: 423 ALHGELLEQPWLHSADFHT 441


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: 533
Number of extensions: 21
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: 509
Length of database: 457
Length adjustment: 34
Effective length of query: 475
Effective length of database: 423
Effective search space:   200925
Effective search space used:   200925
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: 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