GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Pseudomonas simiae WCS417

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate GFF3807 PS417_19495 N-acyl-L-amino acid amidohydrolase

Query= curated2:Q04FS2
         (382 letters)



>FitnessBrowser__WCS417:GFF3807
          Length = 448

 Score =  181 bits (458), Expect = 5e-50
 Identities = 135/397 (34%), Positives = 198/397 (49%), Gaps = 41/397 (10%)

Query: 7   LIKIRRHLHANPEIGMQEVKTHQFLLEQIAKFPQENLTIETISEIP-TALLVRIAGSDPK 65
           +++ RR +HA+PE+G  E +T + + +Q+      +L +E  + +  T ++  + G+ P 
Sbjct: 48  MLETRRDIHAHPELGNTETRTAELVAKQL-----RDLGLEVKTGVARTGVVAVLKGALPG 102

Query: 66  RTIALRTDMDALPIQEETGLDFASKND--------HVMHACGHDIHMTVALG---ILSYF 114
            T+ALR DMDALP++E   L FASK           VMHACGHD H+ + L    IL+  
Sbjct: 103 PTVALRADMDALPVKEVADLPFASKAKGTYLGKEVDVMHACGHDAHVAILLSTAKILTGM 162

Query: 115 AKHQPKDNLLVFFQPAEE----------NEFGGKRFYDAGGFQGEYLPDEFYALHVNPQL 164
            +  P   +  +FQPAEE          N +G K     G  Q    PD  + LHV   +
Sbjct: 163 RERLP-GTVEFYFQPAEEGPSDFIPDGKNTWGAKMMVQEGVMQSPK-PDAVFGLHVWAGV 220

Query: 165 PAGQIASRKGTLFAGSNELRISFIGKSGHAAYPQNAKDSIVAAANFVTNVQTVVSRNVDP 224
           PAGQIA R G   A S++LRI  +GK  HA  P +  D I   A  +  +QTVVSR  D 
Sbjct: 221 PAGQIAYRSGPTLASSDDLRIKILGKQTHAGRPWDGIDPITVGAQTIVGLQTVVSRRTDI 280

Query: 225 IE-GGVVTIGKFNAGKAMNIIAGKADIEGTIRSFTQSGMEIMTKHIRMIAEGIAGAFGQE 283
                VV+IG  N G   NII    D+ GTIRS+     + +   +R   E IA + G +
Sbjct: 281 SSFPSVVSIGTINGGTRYNIIPESMDMSGTIRSYDYGIRQKLHADVRQTVEKIAESGGAK 340

Query: 284 LKINFRQGGYMPVVNDERTTNFFIDYMKNADGVDFKIVQPAMI--AEDFGFLSNQFEGTM 341
            ++   +  Y P +N+   T   +  ++ A   D  +VQ  ++  AEDF F + +  G  
Sbjct: 341 AEVTIIE-KYDPTINNPALTEKMLPSLRWAAKDD--VVQGPLVGGAEDFSFYAKEAPGLF 397

Query: 342 CWLGV--NDPKHSLHSDHLNP----DESAITKGVEAI 372
            +LGV   D   S  + + NP    DESA+  GV  +
Sbjct: 398 VFLGVTPRDQDMSKAAPNHNPGFFVDESALVVGVRTL 434


Lambda     K      H
   0.320    0.137    0.397 

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: 427
Number of extensions: 24
Number of successful extensions: 6
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: 448
Length adjustment: 31
Effective length of query: 351
Effective length of database: 417
Effective search space:   146367
Effective search space used:   146367
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: 50 (23.9 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