GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Shewanella loihica PV-4

Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate 5211055 Shew_3471 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::Q58991
         (347 letters)



>FitnessBrowser__PV4:5211055
          Length = 364

 Score =  182 bits (462), Expect = 1e-50
 Identities = 125/364 (34%), Positives = 201/364 (55%), Gaps = 29/364 (7%)

Query: 3   KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57
           +V V+ GDGIG EV+ EA K+L  + E      E  + + G   +  +G  LPE T++  
Sbjct: 4   QVAVLAGDGIGPEVMAEARKVLKAVEERFSLDIEYSEYDVGGAAIDHHGCPLPESTLKGC 63

Query: 58  KEADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPIN-NFGIGQLIGKIA 112
           +EAD ILFG++  PK    P   +  +  ++ LR  F L+ N+RP   + G+  +    +
Sbjct: 64  EEADAILFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHVGLEHMSPLRS 123

Query: 113 DYEFLNAKNIDIVIIRENTEDLYVGRERL-----ENDTAIAERVITRKGSERIIRFAFEY 167
           D   ++A+  D++ +RE T  +Y G+ +      E + A      +R+   RI + AFE 
Sbjct: 124 D---ISAQGFDVLCVRELTGGIYFGKPKGRQGEGEQEEAFDTMRYSRREVRRIAKIAFE- 179

Query: 168 AIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKF 226
           A +  RKKV+ + KANVL  +  L+ EV  E+ K + ++  +   +D+  M L++ P  F
Sbjct: 180 AARGRRKKVTSVDKANVLACSV-LWREVVEEVAKEFPDVALEHIYIDNATMQLLRRPFDF 238

Query: 227 DVIVTTNMFGDILSDEASALIGGLGLAPSANIGDDK-ALFEPVHGSAPDIAGKGIANPMA 285
           DV++ +N+FGDI+SDE + L G +GL  S ++  D   L+EP  GSAPDIAG+GIANP+A
Sbjct: 239 DVMLCSNLFGDIISDEIAMLTGSMGLLSSVSLNSDGFGLYEPAGGSAPDIAGQGIANPIA 298

Query: 286 SILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL------GGDLKTKDVGDEILN 338
            ILS A+L  + + E+     I +AV   L +  +T +L           T+++GD I  
Sbjct: 299 QILSAALLLRHSLKEEAAAKAIEDAVAKALSDGYLTGELLPADQRDKAKSTREMGDYIAQ 358

Query: 339 YIRK 342
            +R+
Sbjct: 359 AVRE 362


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: 307
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: 364
Length adjustment: 29
Effective length of query: 318
Effective length of database: 335
Effective search space:   106530
Effective search space used:   106530
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