GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Azoarcus olearius BH72

Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_011764286.1 AZO_RS02775 homocitrate synthase

Query= curated2:Q8RCF9
         (384 letters)



>NCBI__GCF_000061505.1:WP_011764286.1
          Length = 396

 Score =  300 bits (767), Expect = 6e-86
 Identities = 166/372 (44%), Positives = 223/372 (59%), Gaps = 4/372 (1%)

Query: 8   PVYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAK 67
           PV I DTTLRDGEQ+AGV F   EK  IA++L EIG+ +LE+GIP MG +E   +  IA 
Sbjct: 4   PVTIDDTTLRDGEQSAGVAFTRAEKCGIARILAEIGVPELEIGIPAMGSEECGDIRAIAD 63

Query: 68  L----GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMT 123
                G    ++ W R    D+       V  + +S+  SD  I HKL  TR  VL  + 
Sbjct: 64  TLADGGHDTRLIVWGRLTSADIDACRSLPVQMLELSVPVSDQQIRHKLGATRDEVLARIA 123

Query: 124 EAVRFAKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEM 183
             V  A++ G  V V  EDASR D  FL E  + A+ AGA R RF DT+G LDPF T+E 
Sbjct: 124 RWVPVAREAGFDVGVGGEDASRADPAFLAEVIQAAEAAGARRFRFADTLGILDPFATFEA 183

Query: 184 VKAIKDAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMA 243
           ++A++ A  +EIEMH H+D G+ATAN LA V+AGA  V  TVNGLGERAGNAALEEV + 
Sbjct: 184 IRALRAASKLEIEMHAHDDLGLATANTLAAVRAGASHVNTTVNGLGERAGNAALEEVALG 243

Query: 244 LKYVYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYT 303
           L+  + M   ID +R  + SE VA ASGRP+   K++VG+ VF HE+GIHVDG LK+P  
Sbjct: 244 LRQFHGMGEIIDFTRLLDTSEAVARASGRPVGWHKSVVGEGVFTHEAGIHVDGLLKDPAN 303

Query: 304 YEVFDPQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPL 363
           Y+  DP  +G   ++++GKHSG   +   +   G  L       LL  +R+   + KR  
Sbjct: 304 YQGIDPALLGRSHRMLLGKHSGGRGVAAAYAGLGIELDAARTACLLARIREFTSRTKRTP 363

Query: 364 FDKELMYLYEDV 375
             ++L+  +E++
Sbjct: 364 QREDLLAFWEEL 375


Lambda     K      H
   0.318    0.135    0.379 

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: 378
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: 384
Length of database: 396
Length adjustment: 31
Effective length of query: 353
Effective length of database: 365
Effective search space:   128845
Effective search space used:   128845
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: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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