GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Klebsiella michiganensis M5al

Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate BWI76_RS04675 BWI76_RS04675 3-isopropylmalate dehydrogenase

Query= BRENDA::Q58991
         (347 letters)



>FitnessBrowser__Koxy:BWI76_RS04675
          Length = 363

 Score =  191 bits (486), Expect = 2e-53
 Identities = 129/358 (36%), Positives = 197/358 (55%), Gaps = 26/358 (7%)

Query: 4   VCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKAK 58
           + V+ GDGIG EV+ +A+K+L  +           + + G   + + G  LP+ T+E  +
Sbjct: 7   IAVLPGDGIGPEVMNQALKVLEAVRHRFDMRITTSQHDVGGIAIDRQGTPLPQSTVEGCE 66

Query: 59  EADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPINNF-GIGQLIGKIAD 113
           +AD ILFG++  PK    P   +  +  ++ LRK F L++N+RP   + G+ +     AD
Sbjct: 67  QADAILFGSVGGPKWEHLPPAEQPERGALLPLRKHFKLFSNLRPAKLYQGLEEFCPLRAD 126

Query: 114 YEFLNAKNIDIVIIRENTEDLYVGRERL-----ENDTAIAERVITRKGSERIIRFAFEYA 168
              + A   DI+ +RE T  +Y G+ +      +++ A    V  R   ERI   AFE A
Sbjct: 127 ---IAANGFDILCVRELTGGIYFGQPKGREGSGQHEKAFDTEVYHRFEIERIAHIAFESA 183

Query: 169 IKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFD 227
            K  R KV+ I KANVL+ +  L+ E+ +EI K Y ++E     +D+  M LIK P +FD
Sbjct: 184 RKR-RHKVTSIDKANVLQ-SSILWREIVSEISKQYPDVELSHMYIDNATMQLIKDPSQFD 241

Query: 228 VIVTTNMFGDILSDEASALIGGLGLAPSANIGDDK-ALFEPVHGSAPDIAGKGIANPMAS 286
           V++ +N+FGDILSDE + + G +G+ PSA++ +    L+EP  GSAPDIAGK IANP+A 
Sbjct: 242 VLLCSNLFGDILSDECAMITGSMGMLPSASLNEQGFGLYEPAGGSAPDIAGKNIANPIAQ 301

Query: 287 ILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL---GGDLKTKDVGDEILNYI 340
           ILS+A+L  Y +        I  A+   L     T DL      + T ++GD I  Y+
Sbjct: 302 ILSLALLLRYSLDADSAATAIENAINRALEEGVRTGDLARGAAAVSTDEMGDIIARYV 359


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: 294
Number of extensions: 15
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: 347
Length of database: 363
Length adjustment: 29
Effective length of query: 318
Effective length of database: 334
Effective search space:   106212
Effective search space used:   106212
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