GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Pseudomonas putida KT2440

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate PP_0214 PP_0214 4-aminobutyrate aminotransferase

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



>FitnessBrowser__Putida:PP_0214
          Length = 425

 Score =  345 bits (884), Expect = 2e-99
 Identities = 174/416 (41%), Positives = 260/416 (62%), Gaps = 11/416 (2%)

Query: 5   SISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRL 64
           ++ + +  +HPI +   +N+ V D +G+  IDF GGI VLN GH +P VV A+Q Q T++
Sbjct: 15  AVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKV 74

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

Query: 125 FDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSV 184
           F GG+HGRT+ TL L GKV PY   +G +PG ++   +PS   G++ + A+ +++R+F  
Sbjct: 135 FTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKN 194

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

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

Query: 305 QMTDENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANADGSP 359
              +E L       GER    +    +++      P IG + G+G+M  +E F     +P
Sbjct: 315 VFEEEKLLDRSKAVGERLTAGLREIQKKY------PIIGDVRGLGSMIAVEVFEKGTHTP 368

Query: 360 APAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
             A + +V+  AR +GL+L+  G   +++R+L PLT E  +L++GL I+E+C AE+
Sbjct: 369 NAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECFAEI 424


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: 510
Number of extensions: 19
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: 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