GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373
          Length = 430

 Score =  431 bits (1108), Expect = e-125
 Identities = 212/421 (50%), Positives = 283/421 (67%), Gaps = 4/421 (0%)

Query: 1   MNSNKE----LMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTG 56
           MNS  E    L+++R Q +PRG+   HP+  DRA+   +WDV+G+ YLDF GGI VLN G
Sbjct: 1   MNSKVEETPSLLRQRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIG 60

Query: 57  HLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVE 116
           H HPKVVAAV+AQL+K+SH CFQV+AY+PYL+L + + + + G  A K    T+G+EAVE
Sbjct: 61  HNHPKVVAAVQAQLQKISHACFQVVAYKPYLDLAQRLCEMIGGQHAYKAAFFTSGAEAVE 120

Query: 117 NAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLH 176
           NAVKIARA T RS  IAF G +HGRT     LTG   PY    G     V+   YP    
Sbjct: 121 NAVKIARAHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYR 180

Query: 177 GISEDDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIML 236
           G++   A+ ++  +     APE +AAI+IEPVQG+GGF ++   F+Q LRAL  +HGI+L
Sbjct: 181 GVTSAMALQALDELLATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVL 240

Query: 237 IADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGG 296
           I DE+Q+G GRTG  F  +  G+ PDL T AKS+AGG PL+GV G+AE+MDA  PGGLGG
Sbjct: 241 ILDEIQTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGG 300

Query: 297 TYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIA 356
           TY GN ++C AAL V++ +EQE LL +   LG++L+ GLL +  ++P+IGDVRG G M+A
Sbjct: 301 TYGGNALSCAAALAVIEAYEQEQLLARGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLA 360

Query: 357 IELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEI 416
           IEL +  +   PDA L   ++  AR  GL+++ CG Y NVLR L PL   +AQI + L+I
Sbjct: 361 IELIKHDEARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQI 420

Query: 417 I 417
           +
Sbjct: 421 L 421


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: 564
Number of extensions: 22
Number of successful extensions: 1
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: 430
Length adjustment: 32
Effective length of query: 394
Effective length of database: 398
Effective search space:   156812
Effective search space used:   156812
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: 51 (24.3 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