GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3984 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3984
          Length = 651

 Score =  365 bits (937), Expect = e-105
 Identities = 193/454 (42%), Positives = 281/454 (61%), Gaps = 4/454 (0%)

Query: 2   PPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDS 61
           P  + +LVANRGEIA RV++  K +G+T +AV+S  D+ A H++ AD    +G + A DS
Sbjct: 4   PVLTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADS 63

Query: 62  YLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDG 121
           YL I+ +I AA+ +   AIHPGYGFLSENA FA A+E AG+ F+GP +  +  +  K   
Sbjct: 64  YLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAA 123

Query: 122 KRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMD 181
           K L   AGVP  PG  G    ++      E+IGYP+++KA +GGGG G+  V++  QL +
Sbjct: 124 KALMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183

Query: 182 VWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLI 241
                +R A  +FG + + +EKY + PRH+E Q+  D++GN +   ER+C+IQRR+QK++
Sbjct: 184 ALASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243

Query: 242 EEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHP 301
           EEAP+P L  E R +M E  ++  + I Y   GT E    D   +F+F+E+N RLQVEHP
Sbjct: 244 EEAPAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLL-DARGEFFFMEMNTRLQVEHP 302

Query: 302 TTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVT 361
            TE I  +DLV  QI++A GE LP +Q+ +   + G AIE R+ AED  N+F  ++G + 
Sbjct: 303 VTEAITGLDLVAWQIRVARGEALPMTQDQV--PLIGHAIEVRLYAEDPGNDFLPATGRLA 360

Query: 362 YYRE-PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420
            YRE   GPG RVDSG+E G  + P+YD ++ KLI +GE RE A    +  L ++ IGG+
Sbjct: 361 LYRESAAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGL 420

Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFV 454
           KT I   + I+  P F   +  T +I +  +Q +
Sbjct: 421 KTNINFLRRIIGHPAFAAAELDTGFIPRYQEQLL 454


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: 754
Number of extensions: 39
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: 651
Length adjustment: 36
Effective length of query: 473
Effective length of database: 615
Effective search space:   290895
Effective search space used:   290895
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