GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Acidovorax sp. GW101-3H11

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4179
          Length = 459

 Score =  254 bits (648), Expect = 5e-72
 Identities = 152/411 (36%), Positives = 219/411 (53%), Gaps = 18/411 (4%)

Query: 38  IVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFYE 97
           + I++     ++DV+G  F DFA G+ V+N GH H  V+ A+K Q + +TH       YE
Sbjct: 55  LFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQLDLYTHTCFQVVAYE 114

Query: 98  NAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQA 157
             + + E+L  LAPG   +K +   +GAEA E A+K+ +  T R   +AF   +HGRT  
Sbjct: 115 PYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTKRPGVIAFTGGYHGRTNL 174

Query: 158 VLSLTASKWVQQDGFFPTMPGVT-HIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216
            L LT      + GF P  PG T H  +PN                   + L  +E    
Sbjct: 175 TLGLTGKVAPYKIGFGP-FPGETYHALFPNALHGV-----------SVEQALHSVELIFK 222

Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276
             + P  + A   EP+QGEGG+ V P  F   LK  AD YGILL  DEVQ G GRTG ++
Sbjct: 223 NDIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTWF 282

Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI-TFDKPGRHATTFGGNPVAIAAGIEVV 335
           A E + V PDLI   K++ GG PLAGV+ RAD+     PG    T+ G+PVA AA + V+
Sbjct: 283 ASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAVI 342

Query: 336 EIV--KELLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPEL 393
           E    ++LL   Q++G  L + L++   +   IGD RGLG   A+E+ ++ +       L
Sbjct: 343 EAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFENGDLSRPDAAL 402

Query: 394 RDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEEALKA 442
             ++V E+A+RGL+LL CG   N IR + PL  + E +   + I  ++L+A
Sbjct: 403 TKQVVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILADSLEA 453


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: 546
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: 459
Length adjustment: 33
Effective length of query: 412
Effective length of database: 426
Effective search space:   175512
Effective search space used:   175512
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