GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Azospirillum brasilense Sp245

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__azobra:AZOBR_RS19630
          Length = 428

 Score =  286 bits (732), Expect = 9e-82
 Identities = 160/413 (38%), Positives = 236/413 (57%), Gaps = 18/413 (4%)

Query: 36  LPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFF 95
           +P+ ++R E   ++DV+GN F DFA G+ V+N GH HP+++EA+K Q ++FTH       
Sbjct: 22  MPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHTCAMVTP 81

Query: 96  YENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRT 155
           YE+ + LAE+L  L PG   +K  +  +GAEA E A+K+ +  TGR   +AF  AFHGRT
Sbjct: 82  YESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGAFHGRT 141

Query: 156 QAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYV 215
              ++LT      + GF P    V H P+PN YR     D            L  +E+  
Sbjct: 142 LLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDS-----------LKALEQLF 190

Query: 216 FRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKF 275
              V    + AI  EP+QGEGG+ + P  F +AL+K  DE GILL  DE+Q G  RTGK 
Sbjct: 191 KSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGKM 250

Query: 276 WAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEV 334
           +AIEH GVEPDL+   K++ GG PL+ V  +A+I     PG    T+ G+P+A  A + V
Sbjct: 251 FAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGSPLATTAALAV 310

Query: 335 VEIVKE--LLPHVQEVGDYLHKYLEEFKEK--YEVIGDARGLGLAQAVEIVKSKETKEKY 390
           +++++E  L+    ++G+ +        ++    VIGD R LG   A+E+VK + TKE  
Sbjct: 311 LDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTKEPA 370

Query: 391 PELRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALK 441
            EL   +V ++A++GLVLL CG   N IR + PL  +   +D  ++I E +L+
Sbjct: 371 AELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERSLE 423


Lambda     K      H
   0.320    0.141    0.418 

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: 477
Number of extensions: 28
Number of successful extensions: 4
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: 445
Length of database: 428
Length adjustment: 32
Effective length of query: 413
Effective length of database: 396
Effective search space:   163548
Effective search space used:   163548
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 (21.7 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