GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Pseudomonas simiae WCS417

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 GFF3328 PS417_17030 3-methylcrotonyl-CoA carboxylase

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



>FitnessBrowser__WCS417:GFF3328
          Length = 641

 Score =  367 bits (942), Expect = e-106
 Identities = 193/455 (42%), Positives = 282/455 (61%), Gaps = 4/455 (0%)

Query: 1   MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60
           M   + +LVANRGEIA RV++  K MG+T +AV+S  D+ A H++ AD    +G + A D
Sbjct: 1   MSTLTTLLVANRGEIACRVMRTAKAMGLTTVAVHSAIDRDARHSREADIRVDLGGSKATD 60

Query: 61  SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120
           SYL I+ +I AA+ +   AIHPGYGFLSENA FA A+E AG+ F+GP +  +  +  K  
Sbjct: 61  SYLQIDKLIAAAQASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSA 120

Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180
            K L   AGVP  PG  G    ++      E+IGYP+++KA +GGGG G+  V++  QL 
Sbjct: 121 AKALMETAGVPLVPGYHGEAQDLETFRAACERIGYPVLLKATAGGGGKGMKVVEDVSQLA 180

Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240
           +     +R A  +FG   + +EKY + PRH+E Q+  D++G+ +   ER+C+IQRR+QK+
Sbjct: 181 EALASAQREALSSFGNGQMLVEKYLLKPRHVEIQVFADQHGHCLYLNERDCSIQRRHQKV 240

Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300
           +EEAP+P L  E+R++M E  ++  + I Y   GT E    D   +F+F+E+N RLQVEH
Sbjct: 241 VEEAPAPGLSGEQRKAMGEAAVRAAQAIGYVGAGTVEFLL-DARGEFFFMEMNTRLQVEH 299

Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360
           P TE I  +DLV  QI++A GE LP +QE +   + G AIE R+ AED  N+F  ++G +
Sbjct: 300 PVTEAITGLDLVAWQIRVAQGEALPITQEQV--PLTGHAIEVRLYAEDPTNDFLPATGRL 357

Query: 361 TYYREPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419
             YRE   GPG RVDSG+E G  V P+YD ++ KLI +GE RE A    +  L ++ IGG
Sbjct: 358 ALYRESAPGPGRRVDSGVEQGDSVSPFYDPMLGKLIAWGEDREQAQLRLLAMLDEFAIGG 417

Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFV 454
           +KT +   + I+  P F   +  T +I +  ++ +
Sbjct: 418 LKTNLGFLRRIIGHPAFAAAELDTGFIPRYQEELL 452


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: 729
Number of extensions: 35
Number of successful extensions: 4
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: 641
Length adjustment: 36
Effective length of query: 473
Effective length of database: 605
Effective search space:   286165
Effective search space used:   286165
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: 53 (25.0 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