Alignments for a candidate for pccB in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccB in Rhodomicrobium vannielii ATCC 17100

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_013418237.1 RVAN_RS02735 carboxyl transferase domain-containing protein

Query= metacyc::MONOMER-17283
         (535 letters)



>NCBI__GCF_000166055.1:WP_013418237.1
          Length = 535

 Score =  467 bits (1202), Expect = e-136
 Identities = 258/544 (47%), Positives = 347/544 (63%), Gaps = 28/544 (5%)

Query: 6   SHIQPNSPDFQANFAYHQSLAADLR--ERLAQIRQGGGAEQRRRHEERGKLFVRDRIDTL 63
           S I P S  F+AN A   +     R  ER         A+   +   RG+L  R+R+  L
Sbjct: 6   SKIAPGSDAFRANAAAMLAKVEAFRAVERAVIAHSAKAAD---KFAARGQLLPRERVTRL 62

Query: 64  IDPDSSFLEIGALAAYNVYDEEVPA----AGIVCGIGRVAGRPVMIIANDATVKGGTYFP 119
           +DP + FLE+  LA   ++D++  A     G V GIG V+G+ V++ A+D+ +KGGT  P
Sbjct: 63  LDPGTPFLELSTLAGLGMHDDDGEARAMGGGSVIGIGVVSGKRVLVSASDSAIKGGTVSP 122

Query: 120 LTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIP 179
           + ++K LRAQEIA EN+LP IYLV+SGGA L  Q+E+F +    GR F NQA++SA GIP
Sbjct: 123 MGLRKALRAQEIALENKLPLIYLVESGGANLLYQAEMFVEG---GRSFANQARLSAAGIP 179

Query: 180 QIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHT 239
           QIA V GS TAGGAY+P +SD V++V+    IFL GPPLVKAA GE+ T E LGG ++H 
Sbjct: 180 QIAVVHGSSTAGGAYLPGLSDYVILVRDRSKIFLAGPPLVKAAIGEDTTDEALGGTNLHA 239

Query: 240 RISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPE-----PPRYDPREIYGILP 294
            ++G+ ++ A DD  A+ + RD++A L       W+ R P      PP+YD  EI G++P
Sbjct: 240 SVTGLGEFVARDDAHAIQLARDLLAKL------KWD-RAPARAKAAPPKYDAEEILGLVP 292

Query: 295 RDFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESAL 354
              R+ YDVRE+IAR+VDGS   +FK  YG  +VCGFA I GF VGIL NNG +  + + 
Sbjct: 293 VSEREPYDVREIIARLVDGSDFLDFKRDYGAEIVCGFAAINGFEVGILGNNGAIQPDGST 352

Query: 355 KGAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIG 414
           K A F++ C     PLVFLQN TG+MVG   E GG  K G+K++ AV+ A VPKFT+++G
Sbjct: 353 KAAQFMQACDQTGTPLVFLQNTTGYMVGSAAERGGAIKHGSKMIQAVANARVPKFTILVG 412

Query: 415 GSFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQ 474
           GS+GAGNYGMCGR + PR ++ WPNAR++VMGG QAA V+  I R      G    P  +
Sbjct: 413 GSYGAGNYGMCGRGFDPRFIFSWPNARVAVMGGAQAAKVMEMITRAKFEKAGGVNEPVLK 472

Query: 475 ERFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PVQPTRFG 531
           +   A I A+ ++E    YA+ARLWDDG+IDP +TR VL+L L+ AAEA    + P  FG
Sbjct: 473 QMAQA-IEAQLDRESTALYATARLWDDGIIDPCDTRAVLSLCLSLAAEADARKLHPNAFG 531

Query: 532 VFRM 535
           V R+
Sbjct: 532 VARL 535


Lambda     K      H
   0.322    0.139    0.423 

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: 819
Number of extensions: 50
Number of successful extensions: 8
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: 535
Length of database: 535
Length adjustment: 35
Effective length of query: 500
Effective length of database: 500
Effective search space:   250000
Effective search space used:   250000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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