GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Pseudomonas simiae WCS417

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate GFF179 PS417_00900 4-aminobutyrate aminotransferase

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



>FitnessBrowser__WCS417:GFF179
          Length = 425

 Score =  337 bits (863), Expect = 5e-97
 Identities = 173/415 (41%), Positives = 258/415 (62%), Gaps = 4/415 (0%)

Query: 3   QESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQAT 62
           + ++ + +  +HPI     +NA V D +G+ +IDF GGI VLN GH +P ++ A+  Q  
Sbjct: 13  EAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLN 72

Query: 63  RLTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAI 122
           +LTH  F    + PY+ L E+++  VP  +    +L  +G+EA ENA+K+AR ATG+  +
Sbjct: 73  KLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGV 132

Query: 123 IAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLF 182
           IAF G +HGRT+ TL L GKV PY   +G +PG V+   +P+   GV+ + A+ +++R+F
Sbjct: 133 IAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGVFRALFPNELHGVSDDDAIASIERIF 192

Query: 183 SVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQR 242
             +    D+AA I EPVQGEGGF     +F + LR  CD+ GIL+I DE+Q+G GRTG  
Sbjct: 193 KNDAEPRDIAAIIIEPVQGEGGFYVAPKSFMKRLRELCDKHGILLIADEVQTGAGRTGTF 252

Query: 243 FAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALAS 302
           FA  ++G+  DL   AKSIAGG PL  V G+ E M A+  GGLGGTY+G+PI+CAAALA 
Sbjct: 253 FAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAV 312

Query: 303 LAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANAD-GSPA 360
           +    +E+L    +   + +V+  +  +A    P IG +  +GAM  +E F + D   P 
Sbjct: 313 MEVFEEEHLLDRCKAVGERLVTGLKAIQAK--YPVIGEVRALGAMIAVELFDDGDTHKPN 370

Query: 361 PAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            A +A V+  AR +GL+L+  G   +++R+L PLT   E L++GL I+E+C +EL
Sbjct: 371 AAAVASVVAKAREKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECFSEL 425


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: 503
Number of extensions: 23
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: 416
Length of database: 425
Length adjustment: 32
Effective length of query: 384
Effective length of database: 393
Effective search space:   150912
Effective search space used:   150912
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