GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Desulfovibrio vulgaris Hildenborough

Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate 208498 DVU2985 3-isopropylmalate dehydrogenase

Query= BRENDA::Q58991
         (347 letters)



>MicrobesOnline__882:208498
          Length = 357

 Score =  188 bits (478), Expect = 2e-52
 Identities = 122/338 (36%), Positives = 187/338 (55%), Gaps = 20/338 (5%)

Query: 2   MKVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEK 56
           M +C++ GDGIG E++ +  K+L+ +               G   +   G+ LP+ T+E 
Sbjct: 3   MNICLLPGDGIGPEIVAQGTKVLDAVARRFGHTVSTSSALIGGAAIDATGSPLPDATVEA 62

Query: 57  AKEADIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIAD 113
            + +D +L GA+  PK  ++ + K P   ++ +RK   L+AN+RP   F   +L G    
Sbjct: 63  CRTSDAVLLGAVGGPKWDDLPSEKRPEKGLLGIRKALGLFANLRPAALFP--ELAGACLL 120

Query: 114 YEFLNAKNIDIVIIRENTEDLYVGRE-----RLENDTAIAERVITRKGSERIIRFAFEYA 168
              + A  +D+V++RE T D+Y G+      R    T     +       RI R AF+ A
Sbjct: 121 RADIAAAGLDLVVVRELTGDVYFGQPAGIETRDGLRTGFNTMIYDEDEVRRIARVAFDTA 180

Query: 169 IKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFD 227
            +  +++V  + KANVL  T  L+ EV  E+ + Y ++E     VD+ AM L++ P +FD
Sbjct: 181 -RARKRRVCSVDKANVLA-TSRLWREVVEEVARDYPDVELSHMYVDNAAMQLVRWPAQFD 238

Query: 228 VIVTTNMFGDILSDEASALIGGLGLAPSANIGD-DKALFEPVHGSAPDIAGKGIANPMAS 286
           VIVT N+FGDILSDEA+ + G +G+ PSA++G    ALFEP+HGSAPDIAG+  ANP+A+
Sbjct: 239 VIVTGNLFGDILSDEAAVITGSIGMLPSASMGSGGPALFEPIHGSAPDIAGQDKANPIAT 298

Query: 287 ILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL 323
           ILS+ M+     G   + D I  AV+  L     T D+
Sbjct: 299 ILSVGMMLRLGFGLAAEADAIDAAVRRVLAEGYRTGDI 336


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: 317
Number of extensions: 24
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: 357
Length adjustment: 29
Effective length of query: 318
Effective length of database: 328
Effective search space:   104304
Effective search space used:   104304
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