Alignments for a candidate for pccA in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Xanthobacter autotrophicus Py2

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_012113242.1 XAUT_RS06130 urea carboxylase

Query= SwissProt::Q5LUF3
         (681 letters)



>NCBI__GCF_000017645.1:WP_012113242.1
          Length = 1180

 Score =  394 bits (1013), Expect = e-113
 Identities = 248/588 (42%), Positives = 335/588 (56%), Gaps = 45/588 (7%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF K+LIANRGEIA RVI+T R M I +VA++SDAD+    V  ADEAV +GP PA +SY
Sbjct: 1   MFTKVLIANRGEIARRVIRTLRAMNIKSVAVHSDADRFTRGVLEADEAVRLGPAPAAESY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           + +D V+AA +ATGAQAVHPGYGFLSEN  FA+ L  EG+ F+GP    ++  G K T++
Sbjct: 61  LNVDAVIAACKATGAQAVHPGYGFLSENVAFAQRLADEGIRFIGPKPEHLKDFGLKHTAR 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
            +A+ + V  +PG   L+E A+EA+K +  I YPVM+K++AGGGG GM++    QE  + 
Sbjct: 121 ALAKASGVPLLPG-TDLLESAEEALKAAEAITYPVMLKSTAGGGGIGMQLCHTPQELADT 179

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
           F+  +  A  SFGD R+++E+FV + RH+E+Q+  D  G  + LGER+CS+QRRNQKVVE
Sbjct: 180 FERVQRTARASFGDARVYLERFVAEARHVEVQIFGDGKGKVVALGERDCSLQRRNQKVVE 239

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVD-GQKNFYFLEMNTRLQVEHPV 299
           E P+P L +  R ++   AV L ++V Y SAGTVEFI D  ++ FYFLE+NTRLQVEHPV
Sbjct: 240 ETPAPLLSDDVRASLHAAAVQLGQSVAYESAGTVEFIYDPARQEFYFLEVNTRLQVEHPV 299

Query: 300 TELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYR 359
           TE + G+DLVE MIR AAGE      G +   G A+E R+YAE P+  F PS G LT  +
Sbjct: 300 TEAVFGIDLVEWMIRQAAGEDPIAAAGPLAPKGAAMEVRVYAEIPHANFQPSAGLLTEVK 359

Query: 360 PPAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAA 419
            P                      A+ R D  +  G E++ YYDPM+AK+      R AA
Sbjct: 360 FP----------------------ASARIDGWIETGTEVTPYYDPMLAKVIVTGADRQAA 397

Query: 420 IEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAE--EYPEGFEGVNLP-- 475
           I A+  AL    + GI  NL +L A+       S  + T  + +    PE  E V +P  
Sbjct: 398 IAALNAALAETSICGIETNLQYLRAIAASDLLASAKVATTALKDFAFRPESVE-VLVPGA 456

Query: 476 ETDLRRVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGS 535
           ++ L+ +       H          SG MD +  R     V     A+    +    +G 
Sbjct: 457 QSSLQELPGRLHLWH-----VGVPPSGPMDEYSFRRANALV---GNAETACALELTVNGP 508

Query: 536 TVSFDD-------GSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISG 576
           T+ F D       G+ M  T D  P    A   V  A  VL +G ISG
Sbjct: 509 TLRFHDDAVIALSGALMPATLDGIPAPHDAAFAV-MAGQVLAIGAISG 555



 Score = 37.0 bits (84), Expect = 5e-06
 Identities = 24/73 (32%), Positives = 35/73 (47%)

Query: 609  PDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKGVVAKINASAG 668
            PD    +   +PG + KV V     V  G+ +  IE+MKME  + A   G V +I A  G
Sbjct: 1106 PDGCFGVAANVPGNVWKVLVAEETVVAAGETIAIIESMKMEISITAHAAGRVREIRAVPG 1165

Query: 669  NSLAVDDVIMEFE 681
             ++   DV+   E
Sbjct: 1166 RTVRSGDVVCVLE 1178


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: 1898
Number of extensions: 81
Number of successful extensions: 6
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: 1180
Length adjustment: 43
Effective length of query: 638
Effective length of database: 1137
Effective search space:   725406
Effective search space used:   725406
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: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 2024 update 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