GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Sinorhizobium meliloti 1021

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 SM_b21186 SM_b21186 4-aminobutyrate aminotransferase

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__Smeli:SM_b21186
          Length = 422

 Score =  516 bits (1329), Expect = e-151
 Identities = 251/411 (61%), Positives = 312/411 (75%)

Query: 9   RRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQ 68
           R+ +A  RGVG+    +A  AENA + D EGN YIDFAAGIAV+NTGHRHP ++AAV+ Q
Sbjct: 7   RKNAAISRGVGMTTQVYADRAENAEIWDKEGNRYIDFAAGIAVVNTGHRHPKVIAAVKAQ 66

Query: 69  LQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRP 128
           L +FTHT +Q+VPYE+YV LAE++NA+ P     KT F TTGAEAVENAVKIARA TGR 
Sbjct: 67  LDRFTHTCHQVVPYENYVHLAERLNAIVPGDFAKKTIFVTTGAEAVENAVKIARAATGRQ 126

Query: 129 GVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIER 188
            V+AF GGFHGRT+M MALTGKV PYK+GFG  P  V+H P+P +LHG++ + SL A+++
Sbjct: 127 AVVAFGGGFHGRTFMGMALTGKVVPYKVGFGAMPADVFHAPFPIELHGVTVEQSLSALKK 186

Query: 189 LFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTG 248
           LF +D++  +VAAII EPVQGEGGF   P   + A+R +CD+HGI++IADEVQ+GFARTG
Sbjct: 187 LFAADVDPARVAAIIIEPVQGEGGFYPVPTAFMKALREVCDQHGILLIADEVQTGFARTG 246

Query: 249 KLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAH 308
           KLFAM+H+   PDL TMAKSLAGG PL+ V G A IMDAP PGGLGGTY GNPL +AAAH
Sbjct: 247 KLFAMEHHGVAPDLTTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPLGIAAAH 306

Query: 309 AVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSA 368
           AVL++I +E+LCERANQLG RLK  L   +E  P I  +RG G M AVEFND +T  PSA
Sbjct: 307 AVLDVIAEENLCERANQLGNRLKQRLAAIREKAPEIVDIRGPGFMNAVEFNDVRTNLPSA 366

Query: 369 AIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419
             A K++  AL +GL+LLTCG +GNVIRFL P+TI D  F  A+  ++ ++
Sbjct: 367 EFANKVRLLALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDTIEASI 417


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: 609
Number of extensions: 25
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: 421
Length of database: 422
Length adjustment: 32
Effective length of query: 389
Effective length of database: 390
Effective search space:   151710
Effective search space used:   151710
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