GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Marinobacter adhaerens HP15

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate GFF1875 HP15_1832 3-isopropylmalate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__Marino:GFF1875
          Length = 363

 Score =  206 bits (525), Expect = 6e-58
 Identities = 139/359 (38%), Positives = 197/359 (54%), Gaps = 34/359 (9%)

Query: 1   MAYRICLIEGDGIGHEVIPAARRVL----EATGLPLEFVEAEAGWETFERRGTSVPEETV 56
           M   I ++ GDGIG E++  A +VL    +   L L F     G    +   T +P+ET+
Sbjct: 7   MPRTILMLPGDGIGPEIVAEAEKVLNKINDQFNLGLSFESGLVGGAAIDETDTPLPDETL 66

Query: 57  EKILSCHATLFGAATSPT--------RKVPGFFGAIRYLRRRLDLYANVRPAKSRPVPGS 108
           EK     A L GA   P         R   G  G    LR  L+L+AN+RPA   P   S
Sbjct: 67  EKATRADAILLGAVGGPQWDSLPMAKRPEKGLLG----LRSNLELFANLRPAILYPQLAS 122

Query: 109 RP--------GVDLVIVRENTEGLYVEQERRYLDVAIADA------VISKKASERIGRAA 154
                     G+D++IVRE T G+Y  Q R   ++   +         ++    RIGR A
Sbjct: 123 ASSLKPEVVSGLDIMIVRELTGGIYFGQPRGVRELESGERQGYNTYAYTESEIRRIGRVA 182

Query: 155 LRIAEGRPRKTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRP 214
              A+ R +K   +  KANVL +T  L+ + + ++ +++P V +  + VDN AMQLV  P
Sbjct: 183 FEAAQQRGKKLCSV-DKANVLEVTV-LWREIMNDLRREYPDVELSHMYVDNAAMQLVRAP 240

Query: 215 ERFDVIVTTNLLGDILSDLAAGLVGGLGLAPSGNI-GDTTAVFEPVHGSAPDIAGKGIAN 273
           ++FDVIVT N+ GDILSD AA L G +G+ PS ++  +   ++EP HGSAPDIAG+GIAN
Sbjct: 241 KQFDVIVTGNMFGDILSDEAAMLTGSIGMLPSASLNSEKQGMYEPCHGSAPDIAGQGIAN 300

Query: 274 PTAAILSAAMMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331
           P A ILSAAMML Y L E++AA+ +E AV  VL++G RT D+  +   +  T  + EA+
Sbjct: 301 PLATILSAAMMLRYSLNEEKAAEAIEAAVSKVLDQGLRTADIMSEGAKKVSTREMGEAV 359


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: 300
Number of extensions: 17
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: 363
Length adjustment: 29
Effective length of query: 305
Effective length of database: 334
Effective search space:   101870
Effective search space used:   101870
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 Sep 17 2021. The underlying query database was built on Sep 17 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