GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS20550
          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:

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