GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Methylovulum miyakonense HT12

Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_019865912.1 METMI_RS0108805 aspartate aminotransferase family protein

Query= BRENDA::B1XNF8
         (418 letters)



>NCBI__GCF_000384075.1:WP_019865912.1
          Length = 392

 Score =  345 bits (886), Expect = 1e-99
 Identities = 183/394 (46%), Positives = 251/394 (63%), Gaps = 11/394 (2%)

Query: 23  YVMHTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLH 82
           ++M TYGR  V   +GEG  LWD +GK YLD ++GIA C LGHAHPA+ QA+  Q  KL 
Sbjct: 4   HIMPTYGRLAVTFERGEGAWLWDDQGKRYLDALSGIAVCNLGHAHPAVHQALCEQSGKLV 63

Query: 83  HISNLYYIPEQGALAQWIVEHSCADKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142
           H SN+Y I  Q  LA  ++E S  D VFF NSGAEANEAAIKL RKY H +   +E P I
Sbjct: 64  HTSNIYRIALQEQLANRLIEKSGMDNVFFSNSGAEANEAAIKLARKYGHGLG--VENPAI 121

Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYNDIRALEEAITDIDEGNRRVA 202
           +  + SFHGRTLAT++ATG PK Q+ F PL +GF  VPYNDI A+E AI+    G+  + 
Sbjct: 122 IVMEKSFHGRTLATLSATGNPKVQQGFGPLVEGFIRVPYNDIGAVEAAIS----GHGNIV 177

Query: 203 AIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVGVGRTGKYWGYENLGIEP 262
           AI+ E +QGEGGV     +Y   +R +CD++ +LL+LDE+Q G+GRTGK++ Y++ GI P
Sbjct: 178 AILAEPIQGEGGVNIPAADYLNQLRSLCDQHNLLLMLDEIQTGIGRTGKFFAYQHNGILP 237

Query: 263 DIFTSAKGLAGGIPIGAMMCKDSCA-VFNPGEHASTFGGNPFSCAAALAVVETLEQENLL 321
           D+ T AK L  G+PIGA + +   A V   G H STFGGNP +C+AALAV+ TL+ + LL
Sbjct: 238 DVCTVAKALGNGVPIGACLARGKAAEVLTAGTHGSTFGGNPLACSAALAVLATLDADGLL 297

Query: 322 ENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEIKADLELTSIEVVKAAMEKGLLL 381
               ++G  + AG     +  P+  D+R  G++ G+E    L+     +V  A+E GLL+
Sbjct: 298 AAAASKGAAICAGFTGHLQGNPHIVDIRHKGMMIGIE----LDTPCTGLVGQALEAGLLI 353

Query: 382 APAGPKVLRFVPPLIVSAAEINEAIALLDQTLAA 415
                K +R +PPLI+   +I + +  L   ++A
Sbjct: 354 NVTYEKNIRLLPPLIMDELQIQQLVGTLSSLISA 387


Lambda     K      H
   0.319    0.136    0.406 

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: 425
Number of extensions: 18
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: 418
Length of database: 392
Length adjustment: 31
Effective length of query: 387
Effective length of database: 361
Effective search space:   139707
Effective search space used:   139707
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: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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