GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pedobacter sp. GW460-11-11-14-LB5

Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate CA265_RS07530 CA265_RS07530 adenosylmethionine--8-amino-7-oxononanoate transaminase

Query= SwissProt::Q84P52
         (520 letters)



>FitnessBrowser__Pedo557:CA265_RS07530
          Length = 433

 Score =  187 bits (474), Expect = 9e-52
 Identities = 129/433 (29%), Positives = 217/433 (50%), Gaps = 31/433 (7%)

Query: 77  WH-----STDLEPLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLN 131
           WH        L  + I + EG YV+D +GK+Y+DA++  W    G + P +     +QLN
Sbjct: 25  WHPYTQMKNALPHIPIVRGEGVYVFDESGKRYIDAVSSWWVNIHGHSHPYIAQKVAEQLN 84

Query: 132 ELAFYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALG 191
            L  +  F   + +P++ LA+ LL +    K  K F+T++GS A +  +K+   Y +  G
Sbjct: 85  VLE-HVIFAGFTHEPAVLLAERLLPILPG-KQDKVFYTDNGSTAVEVALKMCLQYWDNKG 142

Query: 192 RPDKKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEE 251
            P K K +A   +YHG T  + S+SG       F+     V   D P+ +          
Sbjct: 143 TP-KTKILAFKNAYHGDTFGAMSVSGRSIFTDAFNSLLFDVEFIDLPNEYNI-------- 193

Query: 252 EFSTRLANNLENLILKEGPETIAAFIAEP-VMGAGGVIPPPATYFEKVQAILKKYDILFI 310
              + L ++L NL         A FI EP ++G+GG++   A Y +++ +  K+  IL I
Sbjct: 194 ---SHLTSHLSNL------SDTACFIFEPLILGSGGMLMYEAKYLDQLLSACKEAGILTI 244

Query: 311 ADEVICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKL 370
           ADEV+ GFGR GT F CEK   KPD++ ++K L+ G MP+G    + E+ +   S  +KL
Sbjct: 245 ADEVMTGFGRTGTYFACEKLINKPDIICLSKGLTGGTMPLGVTTCTNEIFEAFLS-DDKL 303

Query: 371 GTFSHGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEIRG 430
            T  HG +++ +P++C  +L +L I  +   ++ + R+  K    L+     P +  IR 
Sbjct: 304 KTLYHGHSFTANPIACVASLASLDILLKSETLQNIKRVEAKHAVFLEEIKTHPKVKAIRQ 363

Query: 431 TGLLHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLEEI 490
           TG +   E+      +        + AYF  +    G+++R  G+ I + PPY++S E++
Sbjct: 364 TGTIIAIEWETGNETSYLSNLRNLLYAYFLDK----GIILRPLGNIIYILPPYVISDEDL 419

Query: 491 DELIIKYGKALKD 503
           D +      AL++
Sbjct: 420 DYIYATIKLALEE 432


Lambda     K      H
   0.317    0.135    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: 527
Number of extensions: 28
Number of successful extensions: 6
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: 520
Length of database: 433
Length adjustment: 33
Effective length of query: 487
Effective length of database: 400
Effective search space:   194800
Effective search space used:   194800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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