GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Pseudomonas putida KT2440

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate PP_1988 PP_1988 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__Putida:PP_1988
          Length = 360

 Score =  200 bits (509), Expect = 4e-56
 Identities = 139/363 (38%), Positives = 200/363 (55%), Gaps = 32/363 (8%)

Query: 1   MAYRICLIEGDGIGHEVIPAARRVLEATG----LPLEFVEAEAGWETFERRGTSVPEETV 56
           M+ +I ++ GDGIG E++  A +VLE       L         G    ++ G  + +ET+
Sbjct: 1   MSKQILILPGDGIGPEIMAEAVKVLELANDKFQLGFSLAHDVIGGAAIDKHGVPLADETL 60

Query: 57  EKILSCHATLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPAKSRPV------ 105
           E+     A L GA   P      R +    G ++ +R +L L+AN+RPA   P       
Sbjct: 61  ERARKADAVLLGAVGGPKWDKIERDIRPERGLLK-IRSQLGLFANLRPAILYPQLADASS 119

Query: 106 --PGSRPGVDLVIVRENTEGLYVEQERRYLDV------AIADAVISKKASERIGRAALRI 157
             P    G+D++IVRE T G+Y    R   ++      A      S+    RI R    +
Sbjct: 120 LKPEIVSGLDILIVRELTGGIYFGAPRGQRELEGGERQAYDTLPYSESEVRRIARVGFDM 179

Query: 158 AEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERF 217
           A  R +K   +  KANVL  +Q L+ + V++VAKD+P V +  + VDN AMQLV  P++F
Sbjct: 180 ARVRGKKLCSV-DKANVLASSQ-LWREVVEDVAKDYPDVELSHMYVDNAAMQLVRAPKQF 237

Query: 218 DVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIANPTA 276
           DV+VT N+ GDILSD A+ L G +G+ PS ++  D   ++EP HGSAPDIAG GIANP A
Sbjct: 238 DVMVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSAPDIAGLGIANPLA 297

Query: 277 AILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDAT----TEAFTEAVVEAL 331
            ILS +MML Y   +  AA+ +EKAV LVL++G RT D+  +      T+   +AVV AL
Sbjct: 298 TILSVSMMLRYSFNQSAAAEAIEKAVSLVLDQGLRTGDIFSEGCRKVGTQEMGDAVVAAL 357

Query: 332 KSL 334
           ++L
Sbjct: 358 RNL 360


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: 294
Number of extensions: 15
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: 360
Length adjustment: 29
Effective length of query: 305
Effective length of database: 331
Effective search space:   100955
Effective search space used:   100955
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