Alignments for a candidate for pccA in Methylobacterium sp. 4-46

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Methylobacterium sp. 4-46

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012332185.1 M446_RS11025 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= metacyc::MONOMER-13589
         (666 letters)



>NCBI__GCF_000019365.1:WP_012332185.1
          Length = 662

 Score =  493 bits (1269), Expect = e-143
 Identities = 293/670 (43%), Positives = 387/670 (57%), Gaps = 54/670 (8%)

Query: 3   KKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSYIV 62
           + +LIANRGEIACR+I+TAR++G++TVAVYS+ADR A HV++ADEA  IGP PA +SY+ 
Sbjct: 5   RSVLIANRGEIACRIIRTARRLGLRTVAVYSEADRAAQHVALADEAHPIGPAPAAESYLR 64

Query: 63  IDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSKKL 122
           ID++++A + +GA+ +HPGYGFLSER DFA A   AG+VF+GPP+ AI AMG K  +K L
Sbjct: 65  IDRLLDAARRAGADCIHPGYGFLSERPDFAEACAQAGIVFVGPPAAAIRAMGLKDAAKAL 124

Query: 123 AKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEGFE 182
              AGV  VPGY G   + D     +  IGYPV+IKA AGGGGKGMR   +        E
Sbjct: 125 VARAGVPVVPGYHGPRQEPDFLAAQAAAIGYPVLIKAVAGGGGKGMRRVEAPEAFSAALE 184

Query: 183 SSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIEEA 242
            ++ EA  +FGD R+ +EK+V  PRH+EIQV  D HGN ++L ER+CS+QRR+QKVIEEA
Sbjct: 185 GAQREALGAFGDPRVLVEKYVLSPRHVEIQVFCDAHGNALHLFERDCSLQRRHQKVIEEA 244

Query: 243 PSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQK-----NFYFLEMNTRLQVEH 297
           P+P +    R AMG  A   A+AVGY  AGTVEFI DG++      F+F+EMNTRLQVEH
Sbjct: 245 PAPGMPPEMRAAMGRAAVEAARAVGYVGAGTVEFIADGREGLRPDGFWFMEMNTRLQVEH 304

Query: 298 PVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTR 357
           PVTE ITG+DLVE   RVAAGE LP  Q DL I+G A+E+RLYAEDP   FLPS GRL  
Sbjct: 305 PVTEAITGLDLVEWQFRVAAGEPLPLGQDDLAIDGHAVEARLYAEDPAGGFLPSTGRLRA 364

Query: 358 YRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEV 417
              P         +R D GV EG  +S +YDPMIAK+     TR  A++ +  ALD   V
Sbjct: 365 LALP-----SGEGLRVDAGVREGDTVSPFYDPMIAKVIAHGATRGEALDRLAAALDRTLV 419

Query: 418 EGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGF--QGAVLDEPTLRRVAAAAAAMN 475
            G   N+ F+ A+   P F  G   T FI + + D    +GA +D   +R+  AA  A  
Sbjct: 420 AGPKTNVAFLRALALAPDFRAGRFDTGFI-DRHLDALTGRGAGIDPGAIRQGVAALLARE 478

Query: 476 RVAEIRRTRISGTMNNHERHVG--VDWVVALQGESYHVSIAADREGSTVSFSDGSSLRV- 532
           R+A           +  +   G    + + ++GE++ V +A    G  ++   G   R  
Sbjct: 479 RIAPASPPSPWDLADGFQLGAGRRQAFPILVEGEAHEVVLAWPEGGGALTIEVGGEARAQ 538

Query: 533 -TSDWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEK 591
             +   PG+    ++  GR                                ++AL  P+ 
Sbjct: 539 DRAHVVPGERGVLVVAGGR--------------------------------QVALAPPDP 566

Query: 592 LPPDTSKY-----LLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVK 646
              D         +  PM G +V + VA GD V  GQ LA VEAMKME+ L A   G V 
Sbjct: 567 FDVDLDHIGEGGSVKAPMHGRLVALFVAPGDRVTRGQRLAIVEAMKMEHALTAPSDGEVT 626

Query: 647 KIAAAPGASL 656
           ++ A  GA +
Sbjct: 627 EVTAQAGAQV 636


Lambda     K      H
   0.318    0.134    0.386 

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: 1171
Number of extensions: 56
Number of successful extensions: 5
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: 666
Length of database: 662
Length adjustment: 38
Effective length of query: 628
Effective length of database: 624
Effective search space:   391872
Effective search space used:   391872
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 24 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