GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Pseudomonas fluorescens FW300-N2C3

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate AO356_10715 AO356_10715 4-aminobutyrate aminotransferase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_10715
          Length = 425

 Score =  338 bits (867), Expect = 2e-97
 Identities = 174/417 (41%), Positives = 258/417 (61%), Gaps = 12/417 (2%)

Query: 5   SISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL 64
           ++ + +  +HPI     +NA V D +G+ +IDF GGI VLN GH +P ++ A+ AQ  +L
Sbjct: 15  AVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTAQLNKL 74

Query: 65  THYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIA 124
           TH  F    + PY+ + E+++  VP  +    +L  +G+EA ENA+K+AR ATG+  +IA
Sbjct: 75  THTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIA 134

Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184
           F G +HGRT+ TL L GKV PY   +G +PG ++   YP+   GV+ + ++ +++R+F  
Sbjct: 135 FTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKN 194

Query: 185 ELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244
           +    D+AA I EPVQGEGGF      F + LR  CD+ GIL+I DE+Q+G GRTG  FA
Sbjct: 195 DAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFA 254

Query: 245 FPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLA 304
             ++G+  DL   AKSIAGG PL  V G+ E M A+  GGLGGTY+G+PI+CAAALA + 
Sbjct: 255 MEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVME 314

Query: 305 QMTDENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANAD-GS 358
              +E+L       GER    + +  +++      P IG +  +GAM  +E F N D   
Sbjct: 315 VFEEEHLLDRCKAVGERLVTGLKAIQKKY------PVIGEVRALGAMIAVELFENGDTHK 368

Query: 359 PAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
           P  A +A+V+  AR +GL+L+  G   +++R+L PLT   E L++GL I+E+C +EL
Sbjct: 369 PNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEECFSEL 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: 500
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