GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Azospirillum brasilense Sp245

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__azobra:AZOBR_RS19630
          Length = 428

 Score =  516 bits (1329), Expect = e-151
 Identities = 255/424 (60%), Positives = 319/424 (75%), Gaps = 3/424 (0%)

Query: 1   MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60
           MSN  F  RR +A PRG+      +   AENA L DVEGN +IDFA GIAVLNTGHRHP 
Sbjct: 1   MSNQSFQDRRNAAVPRGLANAMPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPK 60

Query: 61  LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120
           ++ AV+ QL +FTHT   + PYES+VTLAE++NAL P S   KTAFFTTGAEAVENAVKI
Sbjct: 61  IIEAVKAQLDRFTHTCAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKI 120

Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180
           ARAHTGRPGVIAFSG FHGRT + MALTGKV PYK+GFGPFP  VYH P+P+   G+S Q
Sbjct: 121 ARAHTGRPGVIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQ 180

Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240
           DSL A+E+LFKSD++A +VAAII EPVQGEGGFN+AP E + A+R++CDE+GI++I DE+
Sbjct: 181 DSLKALEQLFKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEI 240

Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300
           Q+GFARTGK+FA++H   +PDLMTMAKSLAGG PLS V G A IMDAP PGG+GGTYAG+
Sbjct: 241 QTGFARTGKMFAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGS 300

Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTL--IDAKESVPAIAAVRGLGSMIAVEF 358
           PLA  AA AVL++I++E L +R+N LG+R+      +  + ++  I  VR LG MIA+E 
Sbjct: 301 PLATTAALAVLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMEL 360

Query: 359 -NDPQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQD 417
             D  T EP+A + + +  +A  +GL+LL+CG YGNVIR L PLT  DA  D  + I++ 
Sbjct: 361 VKDRGTKEPAAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIER 420

Query: 418 ALSD 421
           +L +
Sbjct: 421 SLEE 424


Lambda     K      H
   0.319    0.134    0.388 

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: 579
Number of extensions: 22
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: 421
Length of database: 428
Length adjustment: 32
Effective length of query: 389
Effective length of database: 396
Effective search space:   154044
Effective search space used:   154044
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.

Links

Downloads

Related tools

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