Alignments for a candidate for gcvP in Methylococcus capsulatus Bath

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Methylococcus capsulatus Bath

Align Probable glycine dehydrogenase (decarboxylating) subunit 1; EC 1.4.4.2; Glycine cleavage system P-protein subunit 1; Glycine decarboxylase subunit 1; Glycine dehydrogenase (aminomethyl-transferring) subunit 1 (uncharacterized)
to candidate WP_010959710.1 MCA_RS01720 glycine dehydrogenase

Query= curated2:B8GN16
         (451 letters)



>NCBI__GCF_000008325.1:WP_010959710.1
          Length = 453

 Score =  588 bits (1516), Expect = e-172
 Identities = 283/451 (62%), Positives = 348/451 (77%), Gaps = 1/451 (0%)

Query: 1   MPFIPHTETDIQDMLAAIGVNDIEQLFDEIPSALRTGPLNLVPEAMSEMEITRLMHRRAA 60
           MPFIPHTE +++DMLAAIG   I++LF EIP  LR G L  +PEA+SEME+ +LM  RAA
Sbjct: 1   MPFIPHTEAEVRDMLAAIGAGSIDELFAEIPPDLRCGELKDLPEALSEMEVCKLMEERAA 60

Query: 61  QDHVDLNFIGAGAYEHHIPAAVWQIATRGEFYSAYTPYQAEASQGTLQLVYEYQTMMTGL 120
           ++   L F GAGAYEH+IPAAVW+IA RGEFYSAYTPYQAEASQG+LQ+ YEYQ+MM GL
Sbjct: 61  ENRSALCFAGAGAYEHYIPAAVWEIALRGEFYSAYTPYQAEASQGSLQVFYEYQSMMAGL 120

Query: 121 TGMDVSNASLYDGASALAEAVLMSVRANRKSKSHRVLMPATVNPVYRSVTRAIVHGQGIE 180
             MDVSNASLYDGASAL EA+LM++R N +S+S ++L+P ++NPVY+ V R +   Q +E
Sbjct: 121 MAMDVSNASLYDGASALGEAILMALRTNPESRSRKILLPRSLNPVYKRVVRTLTRNQRVE 180

Query: 181 LVEVPFDPATGRVDPKSLAAFEGQDITALVIPQPNFFGVLEEADALTDWAHAQDAQVIGV 240
           LV++ +D + GR+   +L  FEG +  A+VIPQPN FGVLEE D L DWAH   A+ I V
Sbjct: 181 LVDLDYDRSLGRIAENALETFEGGEFAAVVIPQPNHFGVLEEVDVLADWAHRHGARSIAV 240

Query: 241 VNPVSLALLKPPGEWGGKGADIVCGEGQPLGAPLSSGGPYFGFMCCRKEHVRQMPGRIVG 300
           VNP ++ALLKPPGEWG  GAD+ CGEGQPLG PLS+GGPYFGF+C R++ V Q+PGR+VG
Sbjct: 241 VNPTAMALLKPPGEWGEHGADLACGEGQPLGIPLSAGGPYFGFLCSRQDFVHQLPGRLVG 300

Query: 301 RTLDADGRTGFVLTLQAREQHIRRSKATSNICTNQGLVVTAATIHMALLGPEGLERVAAA 360
           RT+D DGR GF LTLQ REQHIRR KATSNICTNQGL+VTAAT++MAL+GP+GL  VAAA
Sbjct: 301 RTVDVDGREGFTLTLQPREQHIRRGKATSNICTNQGLMVTAATLYMALMGPKGLRNVAAA 360

Query: 361 CHANTHALIERLKPL-GVTPAFAGEAFHEIAFRLPRPVRPVLDAMAQQGVLGGYALGDDY 419
           CHAN  AL+ERL  + GV P F    FHE A RLPR    VL  +A++G+LGG+ L  DY
Sbjct: 361 CHANASALLERLTRIDGVEPVFPAPFFHEAAIRLPRAADRVLAGLAERGILGGHVLSADY 420

Query: 420 SDLGDLLLVCATETKTEADLDRYAEVMKAAL 450
            +LGD LL+CATET+   D+DRYA  +   L
Sbjct: 421 PELGDALLICATETRGPEDMDRYAAALAEVL 451


Lambda     K      H
   0.320    0.135    0.401 

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: 606
Number of extensions: 17
Number of successful extensions: 2
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: 451
Length of database: 453
Length adjustment: 33
Effective length of query: 418
Effective length of database: 420
Effective search space:   175560
Effective search space used:   175560
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. 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)
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 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