GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS05495
          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:

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