GapMind for Amino acid biosynthesis

 

Alignments for a candidate for OAT in Pseudomonas stutzeri RCH2

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate GFF4212 Psest_4285 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= BRENDA::Q6LFH8
         (414 letters)



>FitnessBrowser__psRCH2:GFF4212
          Length = 452

 Score =  180 bits (456), Expect = 9e-50
 Identities = 120/405 (29%), Positives = 211/405 (52%), Gaps = 41/405 (10%)

Query: 31  VLKRGKGVFVYDIEDRRYYDFLSAYSSVNQGHCHPDILNAMINQAKKLTICSRAFFS--D 88
           ++ +  GV+++D E  +  D ++    VN G+   +++ A   Q ++L   +  F +   
Sbjct: 34  IITKASGVYLWDSEGHKILDAMAGLWCVNLGYGREELVEAATRQMRELPYYNLFFQTAHP 93

Query: 89  SLGVCERYLTNLF--GYDKVLMMNTGAEASETAYKLCRKWGYEVKKIPENSAKIIVCN-N 145
                 + + ++   G + V    +G+EA++T  ++ R + + +K  P  + K+++   N
Sbjct: 94  PAVALAKAIADIAPAGMNHVFFTGSGSEANDTVLRMVRHY-WAIKGQP--AKKVVIGRWN 150

Query: 146 NFSGRTLGCVSASTDKKCKNNFGPFVPNFLKV--PY------------------DDLEAL 185
            + G T+   S    K         +P    +  PY                  D LE  
Sbjct: 151 GYHGSTIAGASLGGMKAMHEQSDGPIPGIEHIDQPYWFGEGGDMSPEEFGVRIADQLEQK 210

Query: 186 EKELQDPNVCAFIVEPVQGEAGVIVPSDSYFPGVASLCKKYNVLFVADEVQTGLGRTGKL 245
             E+ +  V AFI EP+QG  GVI+P ++Y+P +  +  +Y++LF+ADEV  G GRTG+ 
Sbjct: 211 ILEVGEDKVAAFIAEPIQGAGGVIIPPETYWPRIKEILARYDILFIADEVICGFGRTGEW 270

Query: 246 LCTHHYGVKPDVILLGKALSGGHYPISAILANDDVMLVLKPG---EHGSTYGGNPLAAAI 302
             + +YG++PD++ + K L+ G+ P+  ++  D+V+  L  G    HG TY G+P+AAA+
Sbjct: 271 FGSDYYGLEPDLMPIAKGLTSGYIPMGGVIVRDEVVQTLNEGGEFYHGFTYSGHPVAAAV 330

Query: 303 CVEALKVLINEKLCENADKLGAPFLQNLKEQLKDSKVVREVRGKGLLCAIEF-KNDLV-- 359
            +E +++L  EK+ E      AP+LQ+  ++L D  +V E RG GLL A+E  KN     
Sbjct: 331 ALENIRILREEKIVERVKTKTAPYLQSRWQELLDHPLVGEARGVGLLGALELVKNKKTRE 390

Query: 360 -----NVWDICLKF-KENGLITRSVHDKTVRLTPPLCITKEQLDE 398
                 V  +C +    NGL+ R+V D T+ ++PPL I++EQ+DE
Sbjct: 391 RFADPGVGMLCREHCFRNGLVMRAVGD-TMIISPPLVISEEQIDE 434


Lambda     K      H
   0.320    0.138    0.418 

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: 478
Number of extensions: 20
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: 414
Length of database: 452
Length adjustment: 32
Effective length of query: 382
Effective length of database: 420
Effective search space:   160440
Effective search space used:   160440
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