GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Pseudomonas simiae WCS417

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate GFF4565 PS417_23365 aminotransferase

Query= curated2:Q9KCA8
         (369 letters)



>FitnessBrowser__WCS417:GFF4565
          Length = 364

 Score =  165 bits (418), Expect = 2e-45
 Identities = 108/355 (30%), Positives = 172/355 (48%), Gaps = 26/355 (7%)

Query: 11  PPYKPGKPMEDVKRELGLETVVKLASNENPFGASPKVAEAIQEALHHTAIYPDGYARTLR 70
           PP KP K              V+L  NE+P+G S    EA+Q  +     YP      L 
Sbjct: 30  PPEKPDK--------------VRLNYNESPYGPSGAAREAMQRGIATAGFYPYDSMYALA 75

Query: 71  DKVAHYVGVAPEELIFGNGSDEVIQILCRAFLNEQTNTVMAEPTFSQYKLNAVIEGAELR 130
              A   G+A E++    GS   ++    AF  E    VMA P++   +  A    A ++
Sbjct: 76  GLFAQQQGIAEEQVAVFAGSMAALRYAVLAFTTESRGLVMAMPSYEVPRQAARSNKAPVK 135

Query: 131 EVPL-KDGVHDLDGMLEVIDENTRIVWVCNPNNPTGTYVSAEAFQSFLAKVPEDVLVVSD 189
           EV L  D  HD+  ML   D    +++VCNPNNPTGT    EA +  LA  P+  ++V D
Sbjct: 136 EVSLGADHAHDIPAMLAA-DPQAGMLYVCNPNNPTGTITPTEAIRHALANKPKGSVLVVD 194

Query: 190 EAYVEYVTADDYPDTVPMIRTYKNLVVLRTFSKVFGLAALRIGYGVANQALIEKIEPVRP 249
           EAY+++    D P  V  ++ + +L+VLRTFSK++G+A  R+G  + + AL+E++     
Sbjct: 195 EAYIDFA---DVPSVVSWVKDHDDLLVLRTFSKIYGMAGARLGLAIGHPALLERLAVFGG 251

Query: 250 PFNNSTFSQVAAVAALEDEAFVQSSVEKNNEGMEQLTEWCSRMGLDYFPSQTNFLLIHVN 309
               +  S +  +A+LED   +      NN+  ++   W    G     SQ N  +I V 
Sbjct: 252 DNVPAGTSLLGGLASLEDVKLLPQRKALNNQLRDETVAWLKGRGFTCTASQANCFMIDVK 311

Query: 310 RSSDDVFNAMLKKGYIIRSGRAL-GYPAWIRITIGSKEQNDGCLAALADVLAEEL 363
           + ++ V   +  +G +I  GR    +P W+R+T+G K +    +A   +V A ++
Sbjct: 312 QPAEQVIEKLATQGVMI--GRVFESWPQWVRVTVGDKRE----MARFREVFAAQV 360


Lambda     K      H
   0.317    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: 322
Number of extensions: 13
Number of successful extensions: 5
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: 369
Length of database: 364
Length adjustment: 30
Effective length of query: 339
Effective length of database: 334
Effective search space:   113226
Effective search space used:   113226
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 (21.6 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