GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Acidovorax sp. GW101-3H11

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= reanno::pseudo6_N2E2:Pf6N2E2_4013
         (425 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4179
          Length = 459

 Score =  560 bits (1442), Expect = e-164
 Identities = 280/417 (67%), Positives = 333/417 (79%)

Query: 4   TNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63
           TNA L+ RR AAV RGVGQ H +F + A+NA + DVEGR FIDFAGGIAVLNTGH+H  +
Sbjct: 33  TNAALLTRRHAAVARGVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGV 92

Query: 64  IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA 123
           IAAV  QL+  THTCFQV+AYEPYVE+CE++N   PG FAKK+LL+TTG+EAVENA+KIA
Sbjct: 93  IAAVKAQLDLYTHTCFQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIA 152

Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183
           RA T R GVIAFTG YHGRT +TLGLTGKV PY  G G  PG  + AL+PN LHGVS++ 
Sbjct: 153 RAYTKRPGVIAFTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQ 212

Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243
           ++ S+E IFKND EP  +AA I+EPVQGEGGFYVAP EF+  L+ L D++GILLIADEVQ
Sbjct: 213 ALHSVELIFKNDIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQ 272

Query: 244 TGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303
           TGAGRTGT+FA EQ  VA DL T AKS+AGGFPLAGV G+A+ MDA APGGLGGTYAGSP
Sbjct: 273 TGAGRTGTWFASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSP 332

Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELFEN 363
           +ACAA+LAV+E F +E LL R + +G  LV  LK +  + P IGDVR LGAM+A+ELFEN
Sbjct: 333 VACAASLAVIEAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFEN 392

Query: 364 GDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEE 420
           GD  +P+AA   QVVA+A  +GLILLSCGT+GNV+R+LVPLTA DE L +GLAIL +
Sbjct: 393 GDLSRPDAALTKQVVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILAD 449


Lambda     K      H
   0.320    0.137    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: 645
Number of extensions: 20
Number of successful extensions: 1
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: 425
Length of database: 459
Length adjustment: 32
Effective length of query: 393
Effective length of database: 427
Effective search space:   167811
Effective search space used:   167811
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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