GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Shewanella amazonensis SB2B

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate 6936139 Sama_0336 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__SB2B:6936139
          Length = 364

 Score =  184 bits (466), Expect = 4e-51
 Identities = 133/340 (39%), Positives = 187/340 (55%), Gaps = 29/340 (8%)

Query: 1   MAYRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAEAGWETFERRGTSVPEETV 56
           M+Y+I ++ GDGIG EV+  AR+VL        L +E+ E + G    +  G  +P+ T+
Sbjct: 1   MSYQIAVLAGDGIGPEVMAEARKVLAEVEARFDLNIEYSEYDVGGIAIDNHGCPLPDATL 60

Query: 57  EKILSCHATLFGAATSPT------RKVPGFFGAIRYLRRRLDLYANVRPAKSR------- 103
           +   +  A LFG+   P        + P   GA+  LR   +L+ N+RPA+         
Sbjct: 61  KGCEAADAILFGSVGGPKWEHLPPNEQPER-GALLPLRGHFELFCNLRPARLHTGLEHMS 119

Query: 104 PVPG--SRPGVDLVIVRENTEGLYV-----EQERRYLDVAIADAVISKKASERIGRAALR 156
           P+    S  G D++ VRE T G+Y       Q     + A      S++   RI + A  
Sbjct: 120 PLRADISAQGFDVLCVRELTGGIYFGKPKGRQGEGEEEEAFDTMRYSRREIRRIAKIAFE 179

Query: 157 IAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPER 216
            A GR  K   +  KANVL  +  L+ + V+EVAKDFP V ++ I +DN  MQL+ RP  
Sbjct: 180 AARGRRGKVTSV-DKANVLACSV-LWREVVEEVAKDFPDVTLEHIYIDNATMQLLRRPFD 237

Query: 217 FDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIANPT 275
           FDV++ +NL GDILSD  A L G +GL  S ++ G    ++EP  GSAPDIAGKGIANP 
Sbjct: 238 FDVMLCSNLFGDILSDEIAMLTGSMGLLSSASMNGSGFGLYEPAGGSAPDIAGKGIANPI 297

Query: 276 AAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDL 314
           A ILSAA+ML + L ++EAA  +E+AV   LE G  T +L
Sbjct: 298 AQILSAALMLRHSLKQEEAAACIERAVGAALEAGFLTGEL 337


Lambda     K      H
   0.319    0.137    0.391 

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: 298
Number of extensions: 18
Number of successful extensions: 6
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: 334
Length of database: 364
Length adjustment: 29
Effective length of query: 305
Effective length of database: 335
Effective search space:   102175
Effective search space used:   102175
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: 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