GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Pseudomonas fluorescens FW300-N2C3

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate AO356_10715 AO356_10715 4-aminobutyrate aminotransferase

Query= SwissProt::Q5JEW1
         (445 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_10715 AO356_10715
           4-aminobutyrate aminotransferase
          Length = 425

 Score =  261 bits (667), Expect = 3e-74
 Identities = 156/408 (38%), Positives = 221/408 (54%), Gaps = 18/408 (4%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           PI  E  +   V DV+G  F DFA G+ V+N GH HP+++ A+  Q  K TH       Y
Sbjct: 25  PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTAQLNKLTHTCFQVLAY 84

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156
           E  + + EK+    PGD  +K +   +G+EA E A+K+ +  TGR   +AF  A+HGRT 
Sbjct: 85  EPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTM 144

Query: 157 AVLSLTASKWVQQDGFFPTMP-GVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYV 215
             L LT  K V        MP G+    YPN       + G    D + +     IE   
Sbjct: 145 MTLGLT-GKVVPYSAGMGLMPGGIFRALYPNE------LHGVSIDDSIAS-----IERIF 192

Query: 216 FRHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKF 275
                P +I AI  EP+QGEGG+ V PK F K L+   D++GILL  DEVQ G GRTG F
Sbjct: 193 KNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTF 252

Query: 276 WAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRAD-ITFDKPGRHATTFGGNPVAIAAGIEV 334
           +A+E  GV  DL  F K+I GG PLAGV  +A+ +    PG    T+ G+P+A AA + V
Sbjct: 253 FAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAV 312

Query: 335 VEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYPE 392
           +E+ +E  LL   + VG+ L   L+  ++KY VIG+ R LG   AVE+ ++ +T +    
Sbjct: 313 MEVFEEEHLLDRCKAVGERLVTGLKAIQKKYPVIGEVRALGAMIAVELFENGDTHKPNAA 372

Query: 393 LRDRIVKESAKRGLVLLGCG--DNSIRFIPPLIVTKEEIDVAMEIFEE 438
              ++V ++  +GL+LL CG   N +R + PL    E++D  + I EE
Sbjct: 373 AVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEE 420


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: 494
Number of extensions: 32
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: 425
Length adjustment: 32
Effective length of query: 413
Effective length of database: 393
Effective search space:   162309
Effective search space used:   162309
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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