GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Herbaspirillum seropedicae SmR1

Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate HSERO_RS14210 HSERO_RS14210 homocitrate synthase

Query= curated2:Q8RCF9
         (384 letters)



>FitnessBrowser__HerbieS:HSERO_RS14210
          Length = 376

 Score =  344 bits (883), Expect = 2e-99
 Identities = 175/360 (48%), Positives = 235/360 (65%)

Query: 9   VYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIAKL 68
           V I DTTLRDGEQTAGV F   EKI IA+ LDEIG+ ++E+GIP MG  E E +  IA L
Sbjct: 2   VTINDTTLRDGEQTAGVAFTAEEKIDIARALDEIGVPEMEIGIPIMGQAEIEVIQAIAAL 61

Query: 69  GLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAVRF 128
            L++  M W R    D+  +  C  D V +S+  SDIHI+HKL++ R WVL  +   +  
Sbjct: 62  PLRSKTMVWGRMCEADLAAAARCNADIVNLSMPVSDIHIQHKLQRDRDWVLAQIRHFLPK 121

Query: 129 AKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKAIK 188
           A   G+ V +  ED+SR D++F++     A+ AGA R RF DT+G LDPF TYE+++ ++
Sbjct: 122 ALDLGMEVCLGGEDSSRADLDFMLRVIETAQAAGARRFRFADTLGLLDPFATYEVIRQLR 181

Query: 189 DAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKYVY 248
             VDIE+EMH HND G+ATAN LA + AGA  V  TVNGLGERAGNA LEEVVM L++++
Sbjct: 182 QEVDIELEMHAHNDLGLATANTLAAINAGASHVNTTVNGLGERAGNAPLEEVVMGLRHLH 241

Query: 249 KMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEVFD 308
            ++  +DT     IS  VA ASG+ + P+K+IVG+ VF HESGIHVDG LKNP  YE F 
Sbjct: 242 GIETQVDTRSLPAISRLVAKASGKAVAPNKSIVGEAVFTHESGIHVDGLLKNPANYEHFS 301

Query: 309 PQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDKEL 368
           P E+G    IV+GKHSG+  + + F + G +L++ +A  +L  +R   +  K    + EL
Sbjct: 302 PAELGRSHHIVLGKHSGSRGVKDAFAKMGILLSDSQAQAMLMRIRDHTMVAKAAPSEDEL 361


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: 340
Number of extensions: 9
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: 376
Length adjustment: 30
Effective length of query: 354
Effective length of database: 346
Effective search space:   122484
Effective search space used:   122484
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