GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Burkholderia phytofirmans PsJN

Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate BPHYT_RS30235 BPHYT_RS30235 tartrate dehydrogenase

Query= BRENDA::Q5SIJ1
         (334 letters)



>FitnessBrowser__BFirm:BPHYT_RS30235
          Length = 360

 Score =  221 bits (562), Expect = 3e-62
 Identities = 144/356 (40%), Positives = 198/356 (55%), Gaps = 28/356 (7%)

Query: 3   YRICLIEGDGIGHEVIPAARRVLEAT----GLPLEFVEAE-AGWETFERRGTSVPEETVE 57
           YRI +I GDGIG EV+P A R LEA     G+ LE+   E A  + + + G  +P++   
Sbjct: 5   YRIAVIPGDGIGVEVMPEAIRALEAVKTRFGIELEYQHIEWASCDYYAKHGKMMPDDWKA 64

Query: 58  KILSCHATLFGAATSPTRKVP---GFFGAIRYLRRRLDLYANVRPAK-----SRPVPGSR 109
           ++ S  A LFGA   P   VP     +G++   RR  D Y N+RPA+       P+ G R
Sbjct: 65  QLQSADAILFGAVGWPDT-VPDHISLWGSLLKFRREFDQYINLRPARLFAGVPSPLAGRR 123

Query: 110 PG-VDLVIVRENTEGLY-----VEQERRYLDVAIADAVISKKASERIGRAALRIAEGRPR 163
            G +D  IVRENTEG Y     V  E    +  + ++V ++  SER+ + A  +A+ R R
Sbjct: 124 AGDIDFWIVRENTEGEYSSVGGVMFEGTEREFVLQESVFTRHGSERVLKFAFDLAQRRER 183

Query: 164 KTLHIAHKANVLPLTQGLFLDTVKEVAKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTT 223
           K + +A K+N + ++   +      +A  +P V      +D    + V+ P+RFDV+V T
Sbjct: 184 KKITVATKSNGIAISMPWWDKVAAGIAAQYPDVTWDKQHIDILCARFVLSPDRFDVVVAT 243

Query: 224 NLLGDILSDLAAGLVGGLGLAPSGNIGDT---TAVFEPVHGSAPDIAGKGIANPTAAILS 280
           NL GDILSDL     G +GLAPSGN+       ++FEPVHGSAPDIAGK IANP A I S
Sbjct: 244 NLFGDILSDLGPACTGTIGLAPSGNLNPDRKFPSLFEPVHGSAPDIAGKNIANPIAMIWS 303

Query: 281 AAMMLDYLG-----EKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331
           AAMMLD+LG     E+EA   +  A++  L  GP T DLGG A T    +A+   L
Sbjct: 304 AAMMLDFLGNHEGKEREAHDAILAAIEATLVEGPHTGDLGGKANTTEVGQAIAARL 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: 316
Number of extensions: 17
Number of successful extensions: 7
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