GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Escherichia coli BW25113

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 16426 b2319 hypothetical protein (NCBI)

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Keio:16426
          Length = 337

 Score =  310 bits (793), Expect = 4e-89
 Identities = 161/337 (47%), Positives = 218/337 (64%), Gaps = 3/337 (0%)

Query: 1   MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60
           MS+ +N+A+ GATGAVGE +LE L ER+FPV E++ LA   S G+  RF GKT+ VQ+  
Sbjct: 1   MSEGWNIAVLGATGAVGEALLETLAERQFPVGEIYALARNESAGEQLRFGGKTITVQDAA 60

Query: 61  EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120
           EFDW+Q  +A F AG E +A W   A  +G +VID++  F  + D+PLVVPEVNP  + +
Sbjct: 61  EFDWTQAQLAFFVAGKEATAAWVEEATNSGCLVIDSSGLFALEPDVPLVVPEVNPFVLTD 120

Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180
           +RNRN+IA P+  T Q+L ALKP+ D  G+ RI+VT+  S S  GK  +D LAGQ+AKLL
Sbjct: 121 YRNRNVIAVPDSLTSQLLAALKPLIDQGGLSRISVTSLISASAQGKKAVDALAGQSAKLL 180

Query: 181 NGYPA-ETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRV 239
           NG P  E + F +Q+AFN +P +      G  +EE ++V E +KI  D  +M++ + V+ 
Sbjct: 181 NGIPIDEEDFFGRQLAFNMLPLLPD--SEGSVREERRIVDEVRKILQDEGLMISASVVQA 238

Query: 240 PVFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVRDAGGKDHVLVGRVR 299
           PVFYGHA+ V+ E   P+ AE+  D   Q + I L    +FPTQV DA G  H+ VG VR
Sbjct: 239 PVFYGHAQMVNFEALRPLAAEEARDAFVQGEDIVLSEENEFPTQVGDASGTPHLSVGCVR 298

Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336
           ND      +  W VADNVR G A  AV+IAE LV++Y
Sbjct: 299 NDYGMPEQVQFWSVADNVRFGGALMAVKIAEKLVQEY 335


Lambda     K      H
   0.319    0.135    0.395 

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: 299
Number of extensions: 8
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: 337
Length of database: 337
Length adjustment: 28
Effective length of query: 309
Effective length of database: 309
Effective search space:    95481
Effective search space used:    95481
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 (21.8 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