GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Cupriavidus basilensis 4G11

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate RR42_RS01125 RR42_RS01125 acetylglutamate kinase

Query= BRENDA::Q87EL2
         (421 letters)



>FitnessBrowser__Cup4G11:RR42_RS01125
          Length = 305

 Score =  116 bits (291), Expect = 8e-31
 Identities = 90/287 (31%), Positives = 143/287 (49%), Gaps = 31/287 (10%)

Query: 6   EISQYLKRFSQLDAKRFAVVKVGGAVLRDDV--DALTSSLSFLQEVGLTPIVLHGAGPQL 63
           E   Y+++F      +  VVK GG  + ++         +  L+ VG+ P+V+HG GPQ+
Sbjct: 27  EALPYIRKFHG----KTIVVKYGGNAMTEEKLKHGFARDVILLKLVGMNPVVVHGGGPQI 82

Query: 64  DEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHATNLQ-LIEALQRNGARATSITG---G 119
           DE L  VG     + G RVT  ETM +V  V      Q ++  + + G +A  +TG   G
Sbjct: 83  DEALKKVGKVGTFIQGMRVTDEETMEVVEWVLGGEVQQDIVMLINQYGGQAVGLTGKDGG 142

Query: 120 VFEAHYL---DQET------YGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQILN 170
           +  A  L   D+E+       G VG I A+N A ++A    A IPVI+ +G +  GQ  N
Sbjct: 143 LIRAKRLKMPDRESPGAFIDIGFVGDIEAINPAVVKALQDDAFIPVISPIGFSDDGQAYN 202

Query: 171 INADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGMKL 230
           INADV A ++  +L+  K++ +T   G++D  G ++  ++ + E E+L     + GGM  
Sbjct: 203 INADVVAGKMAEILKAEKLVMMTNIPGVMDKAGNLLTDLS-AREIEELFADGTISGGM-- 259

Query: 231 KIEQIKHLLDRLPLESSVSITRPAD------LAKELFTHKGSGTLIR 271
            + +I   LD    +S V+     D      L  E+ T +  GT+IR
Sbjct: 260 -LPKISSALD--AAKSGVNSVHIIDGRIEHSLLLEILTEQAFGTMIR 303


Lambda     K      H
   0.320    0.136    0.399 

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: 266
Number of extensions: 14
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: 421
Length of database: 305
Length adjustment: 29
Effective length of query: 392
Effective length of database: 276
Effective search space:   108192
Effective search space used:   108192
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: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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:

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