GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Escherichia coli BW25113

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate 15422 b1302 GABA aminotransferase, PLP-dependent (NCBI)

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__Keio:15422
          Length = 421

 Score =  261 bits (668), Expect = 2e-74
 Identities = 152/405 (37%), Positives = 227/405 (56%), Gaps = 17/405 (4%)

Query: 41  ERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYENAI 100
           +  E   + DV+GN + DFA+G+ V+N GH HP +V A+++Q ++FTH +     YE+ +
Sbjct: 27  QSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYV 86

Query: 101 ILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQAVLS 160
            LAEK+  LAP   + K  +  +GAEA E A+K+ +  TGR   +AF   FHGRT   ++
Sbjct: 87  TLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMTMA 146

Query: 161 LTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVFRHVP 220
           LT      + GF P    V H+PYP+   +  GI         T   LD IE      + 
Sbjct: 147 LTGKVAPYKIGFGPFPGSVYHVPYPS---DLHGIS--------TQDSLDAIERLFKSDIE 195

Query: 221 PHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFWAIEH 280
             ++ AI FEP+QGEGG+ V PK    A+++  DE+GI++  DEVQ G  RTGK +A++H
Sbjct: 196 AKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDH 255

Query: 281 FGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVVEIV- 338
           +  +PDL+   K++ GG+PL+GV+  A+I     PG    T+ GNP+A+AA   V+ I+ 
Sbjct: 256 YADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIID 315

Query: 339 -KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPELRDRI 397
            + L     ++G  L   L + KE    I   RGLG   AVE     +T E    +  +I
Sbjct: 316 KESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEF-NDPQTGEPSAAIAQKI 374

Query: 398 VKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEAL 440
            + +  +GL+LL CG   N IRF+ PL +   + D AM+I ++AL
Sbjct: 375 QQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419


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: 476
Number of extensions: 23
Number of successful extensions: 5
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: 421
Length adjustment: 32
Effective length of query: 413
Effective length of database: 389
Effective search space:   160657
Effective search space used:   160657
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.

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