GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hicdh in Shewanella sp. ANA-3

Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate 7025740 Shewana3_2890 isocitrate dehydrogenase (RefSeq)

Query= BRENDA::Q945K7
         (374 letters)



>FitnessBrowser__ANA3:7025740
          Length = 336

 Score =  329 bits (844), Expect = 6e-95
 Identities = 164/332 (49%), Positives = 226/332 (68%), Gaps = 3/332 (0%)

Query: 45  TATLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEIDPRTQSFLTWESLESVRRNK 104
           T T+ PGDGIGP I +S  K+   AG   E+E    G     +    L   +LE + +N+
Sbjct: 5   TITVIPGDGIGPSIIDSALKILDKAGCDFEYEFADAGLTALEKQGELLPQRTLELIEKNR 64

Query: 105 VGLKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSLPGYKTRYDDVDLITIRENTEGE 164
           + LKGP+ TP+G+G  S+N+TLRK+  LYANVRP  S  G + RY+++D+IT+RENTEG 
Sbjct: 65  ITLKGPLTTPVGEGFTSINVTLRKKFGLYANVRPVLSFKGTQARYENIDIITVRENTEGM 124

Query: 165 YSGLEHQVVRG--VVESLKIITRQASLRVAEYAFLYAKTHGRERVSAIHKANIMQKTDGL 222
           YSG   +V       E+  I+TRQ + ++A +A+  A+   R++V+ +HKANIM+ T GL
Sbjct: 125 YSGHGQKVSEDGTTAEATSIVTRQGAEQIATFAYELARKENRKKVTIVHKANIMKSTSGL 184

Query: 223 FLKCCREVAEKYPEITYEEVVIDNCCMMLVKNPALFDVLVMPNLYGDIISDLCAGLVGGL 282
           FLK  REV+++YP+I  EE+++D  CM LV NP  FDV+V  NL+GDI+SDLCAGLVGGL
Sbjct: 185 FLKVAREVSQRYPDIKTEEMIVDATCMKLVMNPENFDVIVTTNLFGDILSDLCAGLVGGL 244

Query: 283 GLTPSCNIGEDGVALAEAVHGSAPDIAGKNLANPTALLLSGVMMLRHLKFNEQAEQIHSA 342
           G+ P  NIG D  A+ EAVHGSAPDIAGKNLANPT+++L+ + ML +L   ++A+ I  A
Sbjct: 245 GMAPGANIGRD-AAIFEAVHGSAPDIAGKNLANPTSVILASIQMLEYLGMADKADLIRKA 303

Query: 343 IINTIAEGKYRTADLGGSSTTTEFTKAICDHL 374
           +   I EG   T DLGG+  TT+FT+A+ D L
Sbjct: 304 VSAVIEEGDRTTRDLGGTHGTTDFTQAVLDRL 335


Lambda     K      H
   0.318    0.134    0.389 

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: 11
Number of successful extensions: 3
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: 374
Length of database: 336
Length adjustment: 29
Effective length of query: 345
Effective length of database: 307
Effective search space:   105915
Effective search space used:   105915
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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