GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvP in Azospirillum brasilense Sp245

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 AZOBR_RS10455 AZOBR_RS10455 glycine dehydrogenase

Query= curated2:Q9A354
         (524 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS10455 AZOBR_RS10455 glycine
           dehydrogenase
          Length = 522

 Score =  715 bits (1846), Expect = 0.0
 Identities = 364/526 (69%), Positives = 413/526 (78%), Gaps = 8/526 (1%)

Query: 1   MNNVGRPTRPEAANDAANGHETLTGARGLLQDEALIFELDGWNKTGVDLPPVTAAPSSDL 60
           MNN GRPT     +D+A   +T+TG RGL  +E LIFE D   + GVDLP V A  +S L
Sbjct: 3   MNNQGRPTGLAEGSDSAVP-QTVTGNRGLQIEEPLIFEQDSVGRCGVDLPEVPAV-ASRL 60

Query: 61  NGLLRDAPIGLPGLSEPETVRHYVRLSQKNHAIDLALYPLGSCTMKHNPRLNEKMARLPG 120
             +     IGLPGL+EP+ VRHY RLSQKN+AID  LYPLGSCTMKHNPRLNEKMARLPG
Sbjct: 61  GAVKPRGRIGLPGLAEPQVVRHYTRLSQKNYAIDSGLYPLGSCTMKHNPRLNEKMARLPG 120

Query: 121 FSDIHPLQPQSTVQGALELMDRLAHWLKTLTGMPAVALTPKAGAHGELCGLLAIRAAHEA 180
           F+D+HPLQP+STVQGALELM  L  WL TLTGM AV L P AGAHGE+CG++AIR+AH+A
Sbjct: 121 FADVHPLQPESTVQGALELMAELGRWLATLTGMAAVTLAPAAGAHGEMCGIMAIRSAHDA 180

Query: 181 AGNGHRKTVLAPTSAHGTNPATAAFVGYTVVEIAQTEDGRVDLADLESKLGDHVAAIMVT 240
            G+  R  +L P SAHGTNPATAA  GY V  I  TEDGRVDL  L++KLG  VA +M+T
Sbjct: 181 KGDKGRTKILVPESAHGTNPATAAACGYAVEAIPATEDGRVDLEALKAKLGPDVAGLMLT 240

Query: 241 NPNTCGLFERDVVEIARLTHAAGAYFYCDGANFNAIVGRVRPGDLGVDAMHINLHKTFST 300
           NPNTCGLFERD++ IA   HAAGAYFYCDGANFNAIVGRVRP DLG+D MHINLHKTFST
Sbjct: 241 NPNTCGLFERDIITIAEAVHAAGAYFYCDGANFNAIVGRVRPADLGIDVMHINLHKTFST 300

Query: 301 PHGGGGPGAGPVVLSEALAPFAPTPWLTHG-DNGFELAEHAGDDDAKTAFGRMSAFHGQM 359
           PHGGGGPG+GPVV +E+LAPF P P++    D  F L E AGD     AFGRM AFHGQM
Sbjct: 301 PHGGGGPGSGPVVFAESLAPFVPVPYVVQDKDGAFRLVEQAGDG---PAFGRMKAFHGQM 357

Query: 360 GMYVRAYAYMLSHGADGLRQVAEDAVLNANYIKAQLKDVMSPAFPEGPCMHEALFDDSWL 419
           GM+VRA AYM+SHGADGLRQVA DAVLNANY+ A+L+DVM+P+F EGPCMHE LFDD +L
Sbjct: 358 GMFVRALAYMMSHGADGLRQVANDAVLNANYLLARLQDVMTPSF-EGPCMHECLFDDRFL 416

Query: 420 EGTGVTTLDFAKAMIDEGFHPMTMYFPLVVHGAMLIEPTETESKHELDRFIAALRALAGA 479
           +GTGVTTLD AKA+IDEGFHPMTMYFPLVVHGA+LIEPTETESK  LD+F+ ALRALA  
Sbjct: 417 KGTGVTTLDIAKALIDEGFHPMTMYFPLVVHGALLIEPTETESKASLDQFVTALRALAER 476

Query: 480 AKAGDTERFKGAPFHAPLRRLDETQAARKPRLRWKP-VAAAPLAAE 524
           AK+GD   F+GAP   P RRLDET AARKP LRW P V    +AAE
Sbjct: 477 AKSGDVAYFQGAPRLTPRRRLDETAAARKPVLRWSPAVEPEKVAAE 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: 916
Number of extensions: 37
Number of successful extensions: 5
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: 522
Length adjustment: 35
Effective length of query: 489
Effective length of database: 487
Effective search space:   238143
Effective search space used:   238143
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 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