Alignments for a candidate for gcvP in Rhodospirillum centenum SW SW; ATCC 51521

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Rhodospirillum centenum SW SW; ATCC 51521

Align Probable glycine dehydrogenase (decarboxylating) subunit 2; EC 1.4.4.2; Glycine cleavage system P-protein subunit 2; Glycine decarboxylase subunit 2; Glycine dehydrogenase (aminomethyl-transferring) subunit 2 (uncharacterized)
to candidate WP_012568784.1 RC1_RS17505 aminomethyl-transferring glycine dehydrogenase subunit GcvPB

Query= curated2:Q9A354
         (524 letters)



>NCBI__GCF_000016185.1:WP_012568784.1
          Length = 528

 Score =  720 bits (1858), Expect = 0.0
 Identities = 369/526 (70%), Positives = 414/526 (78%), Gaps = 9/526 (1%)

Query: 1   MNNVGRPTRPEAANDAANGHETLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDL 60
           MN+ GRPT P   + A+   +T TG R L+Q+E L+FELD     GVDLP     P+++L
Sbjct: 3   MNSQGRPTTPHVPS-ASEVAQTHTGNRALMQEEPLLFELDNPGVCGVDLPE---PPTAEL 58

Query: 61  N-GLLRD-APIGLPGLSEPETVRHYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARL 118
             G +R    + LP +SEPE VRHY RLSQKN  ID  +YPLGSCTMKHNPRLNEKMARL
Sbjct: 59  RLGKVRPRGTLALPSVSEPEVVRHYTRLSQKNFGIDSTMYPLGSCTMKHNPRLNEKMARL 118

Query: 119 PGFSDIHPLQPQSTVQGALELMDRLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAH 178
           PGFSDIHPLQP STVQGALEL+D LAHWLKTLTGMPAVA++P AGAHGELCGL+AIRAA 
Sbjct: 119 PGFSDIHPLQPVSTVQGALELIDALAHWLKTLTGMPAVAMSPAAGAHGELCGLMAIRAAL 178

Query: 179 EAAGNGHRKTVLAPTSAHGTNPATAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIM 238
            A G  HR+ VL P SAHGTNPATAAF G+ V  I   +DGRV +A +++KLG  VAAIM
Sbjct: 179 AARGEAHRRRVLVPESAHGTNPATAAFCGFAVDSIPAEDDGRVSVAAVKAKLGPDVAAIM 238

Query: 239 VTNPNTCGLFERDVVEIARLTHAAGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTF 298
           +TNPNTCGLFE  + EIA   HAAG YFYCDGAN+NAIVGRVRP DLGVDAMHINLHKTF
Sbjct: 239 LTNPNTCGLFEPQIREIADAVHAAGGYFYCDGANYNAIVGRVRPADLGVDAMHINLHKTF 298

Query: 299 STPHGGGGPGAGPVVLSEALAPFAPTPWLTHGDNGFELAEHAGDDDAKTAFGRMSAFHGQ 358
           STPHGGGGPG+GPVVLS ALAPFAP P++ HG++GF L EHAG+ +    FGRM  FHGQ
Sbjct: 299 STPHGGGGPGSGPVVLSAALAPFAPLPYVVHGEDGFRLVEHAGEAEGH-PFGRMKGFHGQ 357

Query: 359 MGMYVRAYAYMLSHGADGLRQVAEDAVLNANYIKAQLKDVMSPAFPEGPCMHEALFDDSW 418
           MGM+VRA AYMLSHG DGLRQ A DAVLNANY+ A LKDVMS +F EGPCMHEALFDD +
Sbjct: 358 MGMFVRALAYMLSHGGDGLRQAASDAVLNANYVLASLKDVMSASF-EGPCMHEALFDDRF 416

Query: 419 LEGTGVTTLDFAKAMIDEGFHPMTMYFPLVVHGAMLIEPTETESKHELDRFIAALRALAG 478
           L+GTG+T LDFAKA+IDEGFHPMTMYFPLVV GA+LIEPTETESK  LD+FI  LRALA 
Sbjct: 417 LKGTGITPLDFAKALIDEGFHPMTMYFPLVVQGALLIEPTETESKQTLDQFIGTLRALAE 476

Query: 479 AAKAGDTERFKGAPFHAPLRRLDETQAARKPRLRW-KPVAAAPLAA 523
            AK GD E F GAP   P RRLDET AARKP LRW +P  AA  AA
Sbjct: 477 RAKTGDEEYFHGAPRLTPRRRLDETAAARKPVLRWTRPAPAAQAAA 522


Lambda     K      H
   0.318    0.135    0.411 

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: 983
Number of extensions: 37
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: 524
Length of database: 528
Length adjustment: 35
Effective length of query: 489
Effective length of database: 493
Effective search space:   241077
Effective search space used:   241077
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 (21.7 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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