GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Azospirillum brasilense Sp245

Align Homoisocitrate dehydrogenase; HICDH; Homo(2)-isocitrate/homo(3)-isocitrate dehydrogenase; Isohomocitrate dehydrogenase; IHDH; NAD-dependent threo-isohomocitrate dehydrogenase; EC 1.1.1.87; EC 1.1.1.- (characterized)
to candidate AZOBR_RS14130 AZOBR_RS14130 3-isopropylmalate dehydrogenase

Query= SwissProt::Q58991
         (347 letters)



>FitnessBrowser__azobra:AZOBR_RS14130
          Length = 371

 Score =  184 bits (466), Expect = 4e-51
 Identities = 135/374 (36%), Positives = 197/374 (52%), Gaps = 45/374 (12%)

Query: 3   KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57
           K+  + GDGIG EV+ +  ++++ L       F++ +G  G   +  YG  L ++T+  A
Sbjct: 6   KLLFLPGDGIGPEVMRQVRRVIDWLDRKRNVTFDVTEGLVGGAAIDAYGVPLKDETLADA 65

Query: 58  KEADIILFGAITSPKPGEVKNY----KSPIITLRKMFHLYANVRPINNFGIGQLIGKIAD 113
             AD ++ GA+  PK     +Y    ++ +++LRK  +L+AN+RP   F        + D
Sbjct: 66  LAADAVMLGAVGGPKWDNPTDYTKRPEAGLLSLRKELNLFANLRPAVVFDA------LVD 119

Query: 114 YEFLNA---KNIDIVIIRENTEDLYVGRERLENDTAIAER------VITRKGSERIIRFA 164
              L A   K +DI+I+RE T  +Y G  R   D    ER      V T     R+ R A
Sbjct: 120 ASTLKADVIKGLDILIVRELTGGVYFGEPRGITDIGNGERRGVNTQVYTTSEIRRVARVA 179

Query: 165 FEYAIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHYNIEADDYLV-----DSTAMNL 219
           FE A K   K  S + KANV+    GL      E+ K +  E  D  +     D+ AM L
Sbjct: 180 FELARKRGNKLHS-MEKANVME--SGLLWR--QEVTKLHQEEFSDVTLEHMYADNGAMQL 234

Query: 220 IKHPEKFDVIVTTNMFGDILSDEASALIGGLGLAPSANI------GDDKALFEPVHGSAP 273
           +K+P++FDVIVT N+FGDILSDEA+ + G LG+ PSA++      G  KAL+EPVHGSAP
Sbjct: 235 LKNPKQFDVIVTDNLFGDILSDEAAMMTGSLGMLPSASLGAPDANGQRKALYEPVHGSAP 294

Query: 274 DIAGKGIANPMASILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDLGGD----LK 328
           DIAG+ +ANP A++LS AM   Y     E+  ++ +AV+  L     T D+         
Sbjct: 295 DIAGRDLANPCATLLSFAMCLRYSFNMDEEAKMLEKAVQNVLSGGMRTADIMAPGMARCS 354

Query: 329 TKDVGDEILNYIRK 342
           T  +GD IL  + K
Sbjct: 355 TTVMGDSILRELDK 368


Lambda     K      H
   0.319    0.140    0.397 

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: 323
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: 347
Length of database: 371
Length adjustment: 29
Effective length of query: 318
Effective length of database: 342
Effective search space:   108756
Effective search space used:   108756
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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