GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS10455
          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.

Links

Downloads

Related tools

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:

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