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

GapMind for catabolism of small carbon sources

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

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate Ac3H11_1927 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1927
          Length = 670

 Score =  417 bits (1071), Expect = e-120
 Identities = 234/486 (48%), Positives = 316/486 (65%), Gaps = 17/486 (3%)

Query: 4   KILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSYIVI 63
           KILIANR EIA R+I TA +MGI TVA+YSD D  ALHV+ A +AV +G   +  +Y+  
Sbjct: 3   KILIANRSEIARRIIHTAHRMGIETVAVYSDPDASALHVREATQAVALGGAASADTYLRT 62

Query: 64  DKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSKKIA 123
           DK++AA RATGA AVHPGYGFLSEN+ FA+A+   G+ ++GPP  AI A+G K  +K +A
Sbjct: 63  DKLLAAARATGADAVHPGYGFLSENADFAQAVVDAGLTWIGPPPAAIRALGSKAGAKALA 122

Query: 124 QEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREGFQS 183
               V  +PGY G  +  +     + +IG P+M+KA AGGGG+GMR+  +  +      S
Sbjct: 123 VAHCVPCLPGYAGDDQSDERFAAEAARIGTPLMVKAVAGGGGRGMRLVTDLAQLPAALAS 182

Query: 184 SKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVEEAP 243
           +++EA   FG   + IE+ + QPRH+E+Q+  D+HG  I+LGER+CS+QRR+QK++EEAP
Sbjct: 183 ARSEALAGFGCGDLLIERALLQPRHVEVQIFADAHGACIHLGERDCSVQRRHQKIIEEAP 242

Query: 244 SPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVTELI 303
           SP +D A R  MG  AVALA+A GY  AGTVEF++DG  +FY +EMNTRLQVEHPVTE +
Sbjct: 243 SPAVDAALRERMGACAVALAQAAGYVGAGTVEFLLDG-PDFYLMEMNTRLQVEHPVTEAL 301

Query: 304 TGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRPPAE 363
           TG+DLVE  IRVA GEPL +TQ  V L G AIE RL AED +  F P  GR+ ++  P  
Sbjct: 302 TGLDLVEWQIRVARGEPLPLTQDQVHLQGHAIEVRLCAEDAH--FRPHTGRVLQFSAPPA 359

Query: 364 TAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAIEAM 423
           TA         ++  AP    A+R D  + EG E++ +YD M+ KL   APTRA AI A+
Sbjct: 360 TA---------FERAAP---GALRFDHALEEGAEVTPHYDAMLGKLIVHAPTRAEAIAAL 407

Query: 424 RIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLRRVA 483
             AL S  V G+  N  FL+A + HP F +G     F+AE   +  +G+ L   +L+ + 
Sbjct: 408 VRALHSTRVLGLPTNRAFLAACLQHPVFGAGHALVPFLAEHAAQ-LQGL-LSNIELKVLV 465

Query: 484 AAAAAM 489
            +A A+
Sbjct: 466 QSAVAV 471



 Score = 37.7 bits (86), Expect = 2e-06
 Identities = 19/66 (28%), Positives = 33/66 (50%)

Query: 615 LLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKGVVAKINASAGNSLAVD 674
           L  P  G +V + V  GQ +  G  +  IE+MK+E+ L +     VA++  + G  ++  
Sbjct: 596 LRAPFNGKVVALPVAAGQALSAGDTVVVIESMKLEHSLASPVAATVAELLVAPGQQVSPG 655

Query: 675 DVIMEF 680
            V+  F
Sbjct: 656 QVLARF 661


Lambda     K      H
   0.317    0.134    0.387 

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: 1085
Number of extensions: 41
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 681
Length of database: 670
Length adjustment: 39
Effective length of query: 642
Effective length of database: 631
Effective search space:   405102
Effective search space used:   405102
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 (21.7 bits)
S2: 54 (25.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources