GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas putida KT2440

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate PP_4108 PP_4108 putative 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Putida:PP_4108
          Length = 416

 Score =  356 bits (913), Expect = e-103
 Identities = 187/417 (44%), Positives = 259/417 (62%), Gaps = 12/417 (2%)

Query: 13  QAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKK 72
           ++I + +  +HPI      N  VWD +G+ Y+DF GGI VLN GH +P VV A++AQ  +
Sbjct: 4   ESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR 63

Query: 73  LSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTI 132
           L+H  F    + PYL L E ++Q VP  +    +L  +G+EA ENA+K+AR AT +   I
Sbjct: 64  LTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAII 123

Query: 133 AFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFK 192
           AF G +HGRT  TL L GKV PY   +G +PG VY   YP    G++ + A+ ++ R+F 
Sbjct: 124 AFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFS 183

Query: 193 NDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLF 252
            + A ED+AA + EPVQGEGGF A  PAF Q LR  CDE GI++I DE+QSG GRTG  F
Sbjct: 184 VELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRF 243

Query: 253 AMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVL 312
           A  ++G+ PDL   AKSIAGG PL  V GR E+M A+  GGLGGTY+GNPI+C AAL  L
Sbjct: 244 AFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL 303

Query: 313 KVFEQENLLQKANDLGQKLKDGLLAIAEK------HPEIGDVRGLGAMIAIELFEDGDHN 366
                ENL       G++ +  +++  E+       P IG + G+GAM  IE F + D +
Sbjct: 304 AQMTDENLA----TWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIE-FANADGS 358

Query: 367 KPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDE 423
              A+L A+++  AR +GL+L+  G   +++R+L PLTIE   + +GL+I+ QC  E
Sbjct: 359 PAPAQL-AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414


Lambda     K      H
   0.320    0.137    0.401 

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: 525
Number of extensions: 19
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: 426
Length of database: 416
Length adjustment: 32
Effective length of query: 394
Effective length of database: 384
Effective search space:   151296
Effective search space used:   151296
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 Sep 17 2021. The underlying query database was built on Sep 17 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