GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Pseudomonas stutzeri RCH2

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family

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



>FitnessBrowser__psRCH2:GFF2666
          Length = 406

 Score =  196 bits (497), Expect = 1e-54
 Identities = 138/405 (34%), Positives = 205/405 (50%), Gaps = 42/405 (10%)

Query: 21  GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80
           G  + VWD  G+  +DF GGI V  LGH +PA+V A+  QA +L H + N   + P L L
Sbjct: 31  GLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWHIS-NIYTNEPALRL 89

Query: 81  MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG------ATGKRAIIAFDGGFHGRTL 134
            ++L   V  ++       NSGAEA E A K+AR          K  II+    FHGRTL
Sbjct: 90  AKKL---VAATFADRAFFCNSGAEANEAAFKLARRYAHDVYGPQKFEIISALNSFHGRTL 146

Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED-VAA 193
            T+ + G+ + Y    G     + H+PY   +       ALKA         A+ D   A
Sbjct: 147 FTVTVGGQ-SKYSDGFGPKIEGITHVPYNDLE-------ALKA---------AISDKTCA 189

Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253
            + EP+QGE G L  + A+ +  R+ C+E   L+I DE+Q+G GRTG+ FA+   GI PD
Sbjct: 190 VVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTGELFAYMHYGITPD 249

Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLAT 313
           +L  AKS+ GG P+GA++   E+ A L  G  G TY GNP++CA A A +  +    +  
Sbjct: 250 ILTNAKSLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAEAVVDIVNTPEVL- 308

Query: 314 WGERQEQAIVSRYERWKASGLSPYIGRLTGVGAM---RGIEFANADGSPAPAQLAKVMEA 370
                 + + +++ER+KA      IG   GV ++   RG+            +      A
Sbjct: 309 ------EGVKAKHERFKAR--LTQIGERYGVFSLVRGRGLLIGCVLSDAWKGKAGAFCAA 360

Query: 371 ARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
           A    L+++ +G    ++RL   L I+   ++EGLD LE+ +A L
Sbjct: 361 AEKEALMVLQAGP--DVVRLAPSLVIDQADIDEGLDRLERAVAAL 403


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: 450
Number of extensions: 20
Number of successful extensions: 5
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: 406
Length adjustment: 31
Effective length of query: 385
Effective length of database: 375
Effective search space:   144375
Effective search space used:   144375
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