GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuA in Azospirillum brasilense Sp245

Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate AZOBR_RS05495 AZOBR_RS05495 homocitrate synthase

Query= curated2:Q8RCF9
         (384 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS05495 AZOBR_RS05495 homocitrate
           synthase
          Length = 381

 Score =  353 bits (905), Expect = e-102
 Identities = 183/364 (50%), Positives = 245/364 (67%)

Query: 11  IVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKLGL 70
           I DTTLRDGEQTAGV F  +EKI IA+ LDE G+ +LE+GIP MG +E+E +  +A LGL
Sbjct: 9   INDTTLRDGEQTAGVAFTLDEKIAIARALDEAGVPELEIGIPAMGPEEREGIRAVAALGL 68

Query: 71  KASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRFAK 130
           KA +M W R    D++ +L+C V  V +S+  SDIHI  KLK++R W L  +   V+ A+
Sbjct: 69  KARLMVWCRMHDTDLKAALDCKVGTVNLSMPVSDIHITKKLKRSRAWALAEIERKVKTAR 128

Query: 131 KEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIKDA 190
             G+ VS+  ED+SR DM+FLI  A  A++AGA R RF DT+G LDPF+T   ++ ++ A
Sbjct: 129 DHGLEVSLGGEDSSRADMDFLIAAATVAQEAGARRFRFADTLGVLDPFQTRACIERLRRA 188

Query: 191 VDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVYKM 250
            D+EIE+H H+D G+A AN+LA V  GA  V  TVNGLGERAGNA LEEVV++LK +Y  
Sbjct: 189 TDLEIEIHAHDDLGLANANSLAAVLGGATHVNTTVNGLGERAGNAPLEEVVVSLKVLYGQ 248

Query: 251 DLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFDPQ 310
           D G+DT     IS+ V  AS RP+  +K+IVG  VF HE+GIHVDG L++  TY+ FDP 
Sbjct: 249 DCGVDTRALGAISDLVERASNRPVAVNKSIVGDAVFTHEAGIHVDGLLRDRATYQNFDPA 308

Query: 311 EVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDKELMY 370
           EVG E +IV+GKHSGTA +   + + G    +  A  +LP VR +A + KR    +EL  
Sbjct: 309 EVGREHRIVLGKHSGTAGVKMAYGQLGIPCDDATAQAVLPRVRALATRAKRAPTAEELRA 368

Query: 371 LYED 374
            ++D
Sbjct: 369 FHDD 372


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: 385
Number of extensions: 12
Number of successful extensions: 1
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: 381
Length adjustment: 30
Effective length of query: 354
Effective length of database: 351
Effective search space:   124254
Effective search space used:   124254
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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