GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hcs in Klebsiella michiganensis M5al

Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate BWI76_RS16900 BWI76_RS16900 4-hydroxy-2-oxovalerate aldolase

Query= curated2:Q07179
         (382 letters)



>FitnessBrowser__Koxy:BWI76_RS16900
          Length = 338

 Score = 70.1 bits (170), Expect = 9e-17
 Identities = 76/271 (28%), Positives = 113/271 (41%), Gaps = 36/271 (13%)

Query: 5   RTLALCDTTLRDGEQTAGVAFSLAEKKAIARALDRAGVAEIEV-------------GIAA 51
           + L + D TLRDG       +SL   + IARALD AGV  IEV             G  A
Sbjct: 4   KKLYISDVTLRDGMHAIRHQYSLDNVRQIARALDSAGVDSIEVAHGDGLQGSSFNYGFGA 63

Query: 52  ---MGWAEVAEIRAVVAEIAHATPVVWCRLRMHDLDMAQKTGVKRVHFAVPTSTAQLEGK 108
              + W E A      A+IA  T ++     +HDL  A + G + V  A   + A +   
Sbjct: 64  HSDLEWIEAAAESVSQAKIA--TLLLPGIGTLHDLKNAYQAGARVVRVATHCTEADV--- 118

Query: 109 LRVDRDWILRETAALVFCASDRGLQVSVGAEDASRTDPDFLIRLAEVAAAAGAIRFRIAD 168
                      +A  +  A + G+        +  T P+ L + A    + GA    + D
Sbjct: 119 -----------SAQHIAFARELGMDTVGFLMMSHMTAPEQLAQQALKMESYGATCIYVVD 167

Query: 169 TLGLL---DPLGAFRLVAELSARISLPIEMHAHNDFGMATANTIMAAHAGATHLSVTVNG 225
           + G +   D    FR +  +  +      MHAH++  +  AN+I A   G   +  ++ G
Sbjct: 168 SGGAMNMRDIRDRFRALKAV-LKPETATGMHAHHNLSLGVANSIAAVEEGCDRIDASLAG 226

Query: 226 LGERAGNAACEEVGAALEAGGIDTGLDLCAL 256
           +G  AGNA  E   AA +  G + G DL AL
Sbjct: 227 MGAGAGNAPLEVFIAAADKLGWNHGTDLYAL 257


Lambda     K      H
   0.321    0.134    0.392 

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: 262
Number of extensions: 14
Number of successful extensions: 2
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: 382
Length of database: 338
Length adjustment: 29
Effective length of query: 353
Effective length of database: 309
Effective search space:   109077
Effective search space used:   109077
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 (21.9 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