GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Herbaspirillum seropedicae SmR1

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 HSERO_RS20550 HSERO_RS20550 acetyl-CoA carboxylase biotin carboxylase subunit

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS20550 HSERO_RS20550 acetyl-CoA
           carboxylase biotin carboxylase subunit
          Length = 462

 Score =  380 bits (975), Expect = e-110
 Identities = 194/458 (42%), Positives = 298/458 (65%), Gaps = 7/458 (1%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           ++L+ANRGEIA R+++A + +G+T +A  S+AD  ++  + ADE   IG A A  SYLN+
Sbjct: 7   KLLIANRGEIAVRIIRAAQALGITTVAACSDADTDSLAARMADEVQRIGPARADRSYLNV 66

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
           + ++ AA  +  DA+HPGYGFLSENA FAEAV  AG+ F+GP ++ +R++ DK + +R A
Sbjct: 67  DALLKAARDSGADALHPGYGFLSENAAFAEAVNAAGLIFVGPQADTIRRMGDKAEARRTA 126

Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185
             AGVP  PGS G +  +  AL  A++IGYP+++KA++GGGG GI    +  +L   +  
Sbjct: 127 AAAGVPVVPGSAGELEDLATALACADEIGYPLLIKASAGGGGRGIRMARDATELAREFPL 186

Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245
            +  A  AFG A +++E++    RHIE Q++GD     V  +EREC++QRR QK++EEAP
Sbjct: 187 AQAEAQAAFGSAAVYLERFIRRARHIEVQILGDG-ERAVHLFERECSLQRRRQKVLEEAP 245

Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305
           SPAL   +R+++ +  ++  + ++Y   GT E  F D S +F+F+E+N R+QVEHP TE+
Sbjct: 246 SPALTPAQRQALCDSAVRLAERLHYRGAGTLEYLFDDESGEFFFIEMNTRIQVEHPVTEM 305

Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365
           I  IDLV+  +++A GE L   Q D+  R++G A+E RINAED   NF    G V   + 
Sbjct: 306 ITGIDLVQAMLRIAGGEPLGLQQSDI--RMQGAALEMRINAEDPERNFFPCPGTVAELQW 363

Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425
           P G G+RV+S + +G  +PPYYDSL++KL+V+G+ R  AI     A+   +I G+ TT+ 
Sbjct: 364 PQGEGIRVESHLYAGYRIPPYYDSLLAKLVVHGKDRAQAIARAQAAVLATRITGMATTLS 423

Query: 426 LYKWIMQDPDFQEGKFST----SYISQKTDQFVKYLRE 459
           L++W++ D   Q  +F T    ++++++TD   K L E
Sbjct: 424 LHQWLLADARVQSARFDTGALETWLAERTDTRAKQLEE 461


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: 480
Number of extensions: 18
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: 462
Length adjustment: 34
Effective length of query: 475
Effective length of database: 428
Effective search space:   203300
Effective search space used:   203300
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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