GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvP in Azospirillum brasilense Sp245

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 AZOBR_RS10460 AZOBR_RS10460 glycine dehydrogenase

Query= curated2:Q2RPV1
         (448 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS10460 AZOBR_RS10460 glycine
           dehydrogenase
          Length = 446

 Score =  574 bits (1479), Expect = e-168
 Identities = 294/448 (65%), Positives = 347/448 (77%), Gaps = 2/448 (0%)

Query: 1   MRYLPHSEADRAAMLATIGAASVEDLFRDVPREALDQAAFDALPDHGGEMEVERALSALA 60
           MRYLP +EADR +ML  IG  SV++LFRDVP  A      + L +H GE+EV+RALSA+A
Sbjct: 1   MRYLPLTEADRRSMLEAIGVPSVDELFRDVPEAARLSGPIEGLSNHMGELEVDRALSAMA 60

Query: 61  ARNLTAGSVPCFLGAGSYRHHVPAAVDALIQRGEFLTSYTPYQAEVSQGTLQYLFEFQTQ 120
            +NL AGSVP FLGAG+YRHH+PA VD L+QRGEFLT+YTPYQ EVSQGTLQ LFEFQTQ
Sbjct: 61  GKNLPAGSVPSFLGAGAYRHHIPATVDHLVQRGEFLTAYTPYQPEVSQGTLQVLFEFQTQ 120

Query: 121 VALITGMEVANASMYDGATACAEAAAMAVRITRRRKVLMAGGLHPHYTATTQTLLACLGH 180
           V+L+TGM+VANASMYDGATACAEA  MA R+TRR+K +++GGLHPHY  TT T    +G 
Sbjct: 121 VSLLTGMDVANASMYDGATACAEAVMMANRVTRRKKAVLSGGLHPHYRDTTTTDARFIGF 180

Query: 181 EGEGLPPDPLALGDLIGRVGSDTACVIVQNPDFFGRLRDLSPLAEACHAAGALLVVAVCE 240
           E   +PP P    DL+  V  DT+CV+VQNPD FG +RD + L +AC A GALL+V V E
Sbjct: 181 ETVVMPPAPTGGEDLLAAVDGDTSCVVVQNPDVFGHVRDYTELGKACQAKGALLIVVVTE 240

Query: 241 PVSLGLVAPPGAMGADIVVAEGHALGSPTGFGGPGVGLFATREKYLRQMPGRLAGETLDE 300
            VSLGL+ PPG MGADIV AEG +LG+   FGGP VGLFA +EK +RQMPGRL G+T+D 
Sbjct: 241 AVSLGLLTPPGDMGADIVAAEGQSLGNALNFGGPYVGLFAVKEKLVRQMPGRLCGQTVDA 300

Query: 301 SGKRGYVLTLSTREQHIRREKATSNICTNSGLIALAFTIHMTLLGEAGFTRLAWINHANA 360
            G+RG+VLTLSTREQHIRREKATSNICTNSGL ALAF+IH++LLGE GFTRLA INHA A
Sbjct: 301 DGRRGFVLTLSTREQHIRREKATSNICTNSGLCALAFSIHLSLLGEEGFTRLAEINHAKA 360

Query: 361 VALAEKLARVKGVKVLPETFFNEFTLRLPKPAAEVVEALAARSILAGVPVSRFLPTYPEL 420
           V LA+KLA V GV+++ ++FFNEFT++LPKPAAEVVEALA R IL GVP SR       L
Sbjct: 361 VQLADKLAAVTGVEIVNDSFFNEFTVKLPKPAAEVVEALAQRGILGGVPASRLFG--GGL 418

Query: 421 ANLLLVNATELTTPEDADALVAALKEVL 448
            +LL+V ATE  T  D DA   AL EVL
Sbjct: 419 DDLLIVAATETNTESDMDAFATALAEVL 446


Lambda     K      H
   0.320    0.135    0.392 

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: 516
Number of extensions: 18
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: 448
Length of database: 446
Length adjustment: 33
Effective length of query: 415
Effective length of database: 413
Effective search space:   171395
Effective search space used:   171395
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 17 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:

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:

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:

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, or view the source code.

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