GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_10715
          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:

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