GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Acidovorax sp. GW101-3H11

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 Ac3H11_1927 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1927
          Length = 670

 Score =  308 bits (790), Expect = 3e-88
 Identities = 186/492 (37%), Positives = 277/492 (56%), Gaps = 18/492 (3%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           ++L+ANR EIA R++     MG+  +AVYS+ D  A+H + A +A  +G A + D+YL  
Sbjct: 3   KILIANRSEIARRIIHTAHRMGIETVAVYSDPDASALHVREATQAVALGGAASADTYLRT 62

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
           + ++ AA     DA+HPGYGFLSENA+FA+AV  AG+T+IGP    +R +  K   K LA
Sbjct: 63  DKLLAAARATGADAVHPGYGFLSENADFAQAVVDAGLTWIGPPPAAIRALGSKAGAKALA 122

Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185
               VP  PG  G   S +     A +IG P+MVKA +GGGG G+  V +  QL      
Sbjct: 123 VAHCVPCLPGYAGDDQSDERFAAEAARIGTPLMVKAVAGGGGRGMRLVTDLAQLPAALAS 182

Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245
            +  A   FG  DL IE+  + PRH+E Q+  D +G  +   ER+C++QRR+QK+IEEAP
Sbjct: 183 ARSEALAGFGCGDLLIERALLQPRHVEVQIFADAHGACIHLGERDCSVQRRHQKIIEEAP 242

Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305
           SPA+    RE M    +   +   Y   GT E  F     DFY +E+N RLQVEHP TE 
Sbjct: 243 SPAVDAALRERMGACAVALAQAAGYVGAGTVE--FLLDGPDFYLMEMNTRLQVEHPVTEA 300

Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365
           +  +DLV+ QI++A GE LP +Q+ ++  ++G AIE R+ AEDA  +F   +G V  +  
Sbjct: 301 LTGLDLVEWQIRVARGEPLPLTQDQVH--LQGHAIEVRLCAEDA--HFRPHTGRVLQFSA 356

Query: 366 P-------TGPG-VRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKI 417
           P         PG +R D  +E G+ V P+YD+++ KLIV+  +R  AI A +RAL   ++
Sbjct: 357 PPATAFERAAPGALRFDHALEEGAEVTPHYDAMLGKLIVHAPTRAEAIAALVRALHSTRV 416

Query: 418 GGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAEIQSRGLL 477
            G+ T        +Q P F  G     ++++   Q ++ L    E+K  + + +    ++
Sbjct: 417 LGLPTNRAFLAACLQHPVFGAGHALVPFLAEHAAQ-LQGLLSNIELKVLVQSAV---AVI 472

Query: 478 RTSSTDNKGKAQ 489
            +S++     AQ
Sbjct: 473 FSSNSSGAASAQ 484


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: 724
Number of extensions: 29
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: 670
Length adjustment: 36
Effective length of query: 473
Effective length of database: 634
Effective search space:   299882
Effective search space used:   299882
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