Alignments for a candidate for gcvP in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvP in Caulobacter crescentus NA1000

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 CCNA_03463 CCNA_03463 glycine cleavage system protein P, N-terminal domain

Query= curated2:Q0BYP2
         (447 letters)



>FitnessBrowser__Caulo:CCNA_03463
          Length = 448

 Score =  597 bits (1539), Expect = e-175
 Identities = 304/446 (68%), Positives = 347/446 (77%), Gaps = 1/446 (0%)

Query: 1   MRYLPLTPEDRANMLATIGAKSVDDFYTDVPDAARLKGKIAGLPDHQGELAVERHLTKLA 60
           MRYLPLTPEDR  ML  IG KS+DD + DVP +AR    +  LP H GEL VER +  LA
Sbjct: 1   MRYLPLTPEDRVEMLGAIGVKSIDDLFVDVPVSARRDAPV-DLPHHAGELDVEREMAGLA 59

Query: 61  AKNRSASSGPFFVGAGAYKHHVPATVDMIIQRSEFLTTYTPYQPEIAQGTLQTLFEFQTQ 120
            +NR+A  GPFF GAGAY+HHVPATVD IIQRSEFLT+YTPYQPEIAQGTLQ LFEFQTQ
Sbjct: 60  RRNRAAGEGPFFCGAGAYRHHVPATVDHIIQRSEFLTSYTPYQPEIAQGTLQVLFEFQTQ 119

Query: 121 VASLTAMDVANASMYDGSTSCAEAAVMAARVTRRKKIILSGGLHPHYAAATRLLAEAQGL 180
           VA+LT M+VANAS+YDGST  AEA +MA RVTRR K ++SGG+HPHY  A   LA A G+
Sbjct: 120 VAALTGMEVANASLYDGSTGAAEAVMMAQRVTRRNKAVMSGGVHPHYVGAIETLAHAAGV 179

Query: 181 TVVQLPVAIDGEGELAKAVDGETACVIGQSPNVFGTVTDLSAVADAAHGKGALLVSVFTE 240
               LP A+D E  +  A+D +TACV+ Q+PNVFGTVTD+S +A+AAH  GALL+ V TE
Sbjct: 180 ATQALPAAVDAEDAVIAAIDQDTACVVVQTPNVFGTVTDVSKIAEAAHAAGALLIVVTTE 239

Query: 241 AVSLGLVTPPGEMGADIAAGEGQSIGNGLNFGGPYVGLFSCREKLVRQMPGRLCGETVDA 300
           AVS GL+  PGEMGADIA  EGQSIGNGLNFGGPYVGLF+C+EK VRQMPGRLCGETVDA
Sbjct: 240 AVSFGLLKSPGEMGADIAVAEGQSIGNGLNFGGPYVGLFACKEKFVRQMPGRLCGETVDA 299

Query: 301 DGKRGFVLTLSTREQHIRRDKATSNICTNSGLCALAFTSHMTLLGGKGLKQLAELNHEAA 360
           DGKRGFVLTLSTREQHIRRDKATSNICTNSGLCALAF+ HM+LLG  GL+QLA +NH+ A
Sbjct: 300 DGKRGFVLTLSTREQHIRRDKATSNICTNSGLCALAFSIHMSLLGETGLRQLAAVNHQKA 359

Query: 361 IELADALGAVKGVEILTPRFFNEFAIRTPMDAEAVLAMLDEAGVVGGVRASRLFPGDHLG 420
           + L DAL AV GVEILTPRFFNEFAIR P  A  V+ +L   GV+ GV  SRL     L 
Sbjct: 360 LALRDALKAVPGVEILTPRFFNEFAIRVPGKAAEVVEILAAHGVIAGVPFSRLDAKAGLD 419

Query: 421 DVILVAATECTTADDIAAYTDALKEI 446
           DV+LVAATE T   DI  +  AL ++
Sbjct: 420 DVLLVAATETTLDIDIPVFAKALTKV 445


Lambda     K      H
   0.318    0.134    0.382 

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: 617
Number of extensions: 21
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: 447
Length of database: 448
Length adjustment: 33
Effective length of query: 414
Effective length of database: 415
Effective search space:   171810
Effective search space used:   171810
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. 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 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