GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas fluorescens FW300-N2E3

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO353_14875 AO353_14875 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::O67216
         (294 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_14875
          Length = 305

 Score =  130 bits (328), Expect = 3e-35
 Identities = 75/241 (31%), Positives = 134/241 (55%), Gaps = 6/241 (2%)

Query: 2   FQGSIVALITPFK-EGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIE 60
           + G   A+ T F  +  +DYE    +I   V +G   +++CGT GE+ +L+ EE   ++E
Sbjct: 7   WSGVFPAVTTQFNPDFSIDYEGTHKVISGLVRDGVSGLVICGTVGENTSLSTEEKISLVE 66

Query: 61  FAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVV--VPYYNKPTQRGLYEHF 118
            A   AAGR+ VI+G     +  A  +    + VGADG +++  + Y +KP +     HF
Sbjct: 67  VAKDAAAGRVPVISGVAEFTSANASKVAKEIQRVGADGIMLMPALVYSSKPFETA--AHF 124

Query: 119 KTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLG 178
           ++VA  +D+P+++YN P     +++ D +  LA +C+N+V  K+S+ +  R  ++   +G
Sbjct: 125 RSVAASIDLPVMVYNNPPIYRNDVTPDILISLA-DCDNVVCFKDSSGDTRRFIDVRNEVG 183

Query: 179 ESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHD 238
           + F + +G D + L  +A+GA G +S  +N  P+E + L R A +G F+ A  I+ +   
Sbjct: 184 DRFVLFAGLDDVVLESIAVGAVGWVSGMSNAFPKEGETLFRLARDGRFKEAMPIYEWFMP 243

Query: 239 L 239
           L
Sbjct: 244 L 244


Lambda     K      H
   0.318    0.136    0.390 

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: 224
Number of extensions: 12
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: 294
Length of database: 305
Length adjustment: 27
Effective length of query: 267
Effective length of database: 278
Effective search space:    74226
Effective search space used:    74226
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: 48 (23.1 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