GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas fluorescens FW300-N2E2

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Pf6N2E2_670 1-pyrroline-4-hydroxy-2-carboxylate deaminase (EC 3.5.4.22)

Query= BRENDA::Q07607
         (292 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_670
          Length = 305

 Score =  110 bits (274), Expect = 5e-29
 Identities = 74/241 (30%), Positives = 118/241 (48%), Gaps = 6/241 (2%)

Query: 2   FEGSITALVTPFADD-RIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVE 60
           + G   A+ T F DD  I+    H ++   I +G  GLV CG+ GE+ +LS  E   V E
Sbjct: 7   WSGVFPAVTTQFNDDFSINLEKTHQVISNVIRDGVSGLVVCGSVGENTSLSAEEKIAVTE 66

Query: 61  ITIKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSP--YYNKPTQEGIYQHF 118
           + +  + GRVPVI G    ++ +A       +  G DGV+++    Y +KP +    +HF
Sbjct: 67  VAVDASRGRVPVICGVAEFTSVQAAKVANAVRKVGVDGVMLMPALVYGSKPFETA--EHF 124

Query: 119 KAIDAASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVKDATGNLLRPSLERMACG 178
           + +   + +P++VYN P     ++  + L  +  DC NV   KD++G+  R    R   G
Sbjct: 125 RYVARHADVPLMVYNNPPIYKNDVTPDILISL-ADCDNVVCFKDSSGDTRRFIDVRNEVG 183

Query: 179 EDFNLLTGEDGTALGYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDRLMP 238
           + F L  G D   L  +A G  G +S  +NV P       +    G FA A+ + + LMP
Sbjct: 184 DRFVLFAGLDDVVLESLAVGAEGWVSGMSNVFPQEGETIFRLARAGRFAEAMPIYEWLMP 243

Query: 239 L 239
           +
Sbjct: 244 I 244


Lambda     K      H
   0.319    0.136    0.402 

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: 214
Number of extensions: 10
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: 292
Length of database: 305
Length adjustment: 27
Effective length of query: 265
Effective length of database: 278
Effective search space:    73670
Effective search space used:    73670
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: 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