GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Pseudomonas fluorescens GW456-L13

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate PfGW456L13_2301 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)

Query= SwissProt::Q5JEW1
         (445 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301
          Length = 466

 Score =  221 bits (564), Expect = 3e-62
 Identities = 142/425 (33%), Positives = 222/425 (52%), Gaps = 18/425 (4%)

Query: 33  PENLPIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLT 92
           P  +P+ ++R +GI V DV+G  F D  +G G + +GH+HP V+EAI++           
Sbjct: 42  PRRIPLALKRAKGIYVEDVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTL 101

Query: 93  DFFYENAIILAEKLIELAPGDI--ERKVVY-GNSGAEANEAAMKLVKYGTGRKQFLAFYH 149
           D          + L  L P  +  E K+ + G +G +A EAA+KLV+  TGR   ++F  
Sbjct: 102 DLTTPVKDRFVQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVISFQG 161

Query: 150 AFHGRTQAVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLD 209
            +HG +Q  LSL  S   ++        GV  +PYP  YR  +G+ G +         L 
Sbjct: 162 GYHGMSQGALSLMGSLGPKKPLGALLGSGVQFMPYPYDYRCPFGLGGAQG----VKANLS 217

Query: 210 FIEEYVFRHVPPHEI-GAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMG 268
           ++E  +       ++  A+  E +QGEGG +     + + +++  ++ G+ L  DE+Q G
Sbjct: 218 YLENLLNDPEAGVQLPAAVIVEVVQGEGGVIPADLDWLRGVRRITEQAGVALIVDEIQSG 277

Query: 269 IGRTGKFWAIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADITFDKPGRHATTFGGNPVAI 328
             RTGK +A EH G+ PD++   KAIGG LPLA V++R  +    PG HA TF GN +A+
Sbjct: 278 FARTGKMFAFEHAGIIPDVVVMSKAIGGSLPLAVVVYRDWLDTWLPGAHAGTFRGNQMAM 337

Query: 329 AAGIEVVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIV----- 381
           AAG  V+  + E  +  H   +G+ L ++L   +  +  +GD RG GL   VE+V     
Sbjct: 338 AAGCAVMRYLVEHKVCEHAAAMGERLAEHLRILQRDFPQLGDIRGRGLMLGVELVDPTGA 397

Query: 382 -KSKETKEKYPELRDRIVKESAKRGLVLLGCGDNS--IRFIPPLIVTKEEIDVAMEIFEE 438
             ++     +  L   + +E  KRGL+L   G +   +RF+PPL++T  +ID   EIF  
Sbjct: 398 LDAQGHPPAFARLAPLVQRECLKRGLILELGGRHGAVVRFLPPLVITAAQIDRVAEIFGR 457

Query: 439 ALKAA 443
           AL AA
Sbjct: 458 ALAAA 462


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: 517
Number of extensions: 30
Number of successful extensions: 6
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: 466
Length adjustment: 33
Effective length of query: 412
Effective length of database: 433
Effective search space:   178396
Effective search space used:   178396
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