GapMind for Amino acid biosynthesis

 

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

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4179
          Length = 459

 Score =  338 bits (866), Expect = 3e-97
 Identities = 185/411 (45%), Positives = 250/411 (60%), Gaps = 6/411 (1%)

Query: 5   SISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL 64
           ++++ +   H + +   RNAE+WD +G+R+IDF GGI VLN GH +  V+ A++AQ    
Sbjct: 44  AVARGVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQLDLY 103

Query: 65  THYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIA 124
           TH  F    + PY+ + E+L+   P ++    +L  +GAEA ENA+K+AR  T +  +IA
Sbjct: 104 THTCFQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTKRPGVIA 163

Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184
           F GG+HGRT  TL L GKVAPYK   G  PG  YH  +P+A  GV+ EQAL +++ +F  
Sbjct: 164 FTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQALHSVELIFKN 223

Query: 185 ELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244
           ++  E VAAFI EPVQGEGGF    P F   L+   D  GIL+I DE+Q+G GRTG  FA
Sbjct: 224 DIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTWFA 283

Query: 245 FPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLA 304
             +  + PDL+  AKS+AGG PL  VVGR ++M A   GGLGGTY+G+P++CAA+LA + 
Sbjct: 284 SEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAVIE 343

Query: 305 QMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANADGSPAPAQ 363
               E L    +     +V   +   A    P IG + G+GAM  IE F N D S   A 
Sbjct: 344 AFAQEKLLARSQDMGALLVRSLKDLAAR--IPAIGDVRGLGAMVAIELFENGDLSRPDAA 401

Query: 364 LAK--VMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
           L K  V EAAR RGL+L+  G   ++IR+L PLT   E+L EGL IL   L
Sbjct: 402 LTKQVVAEAAR-RGLILLSCGTHGNVIRILVPLTASDELLHEGLAILADSL 451


Lambda     K      H
   0.320    0.137    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: 562
Number of extensions: 24
Number of successful extensions: 2
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: 416
Length of database: 459
Length adjustment: 32
Effective length of query: 384
Effective length of database: 427
Effective search space:   163968
Effective search space used:   163968
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 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