GapMind for catabolism of small carbon sources

 

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

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate PfGW456L13_2301 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2301
          Length = 466

 Score =  224 bits (571), Expect = 4e-63
 Identities = 149/413 (36%), Positives = 220/413 (53%), Gaps = 25/413 (6%)

Query: 29  AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFT--HTAYQIVPYESYV 86
           A+   ++DVEG  +ID  AG   L  GH HP ++ A++Q L      HT     P +   
Sbjct: 52  AKGIYVEDVEGRTFIDCLAGAGTLALGHNHPVVIEAIQQVLADELPLHTLDLTTPVKD-- 109

Query: 87  TLAEKINALAP--VSGQAKTAFF-TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYM 143
              + +  L P  ++ +AK  F   TG +AVE A+K+ R  TGR  VI+F GG+HG +  
Sbjct: 110 RFVQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVISFQGGYHGMSQG 169

Query: 144 TMALTGKVAPYKIGFGPFPGS-VYHVPYPSDLH-------GISTQDSLDAIERLFKSDIE 195
            ++L G + P K   G   GS V  +PYP D             + +L  +E L      
Sbjct: 170 ALSLMGSLGPKK-PLGALLGSGVQFMPYPYDYRCPFGLGGAQGVKANLSYLENLLNDPEA 228

Query: 196 AKQV-AAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMD 254
             Q+ AA+I E VQGEGG   A  + +  +RR+ ++ G+ +I DE+QSGFARTGK+FA +
Sbjct: 229 GVQLPAAVIVEVVQGEGGVIPADLDWLRGVRRITEQAGVALIVDEIQSGFARTGKMFAFE 288

Query: 255 HYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNII 314
           H    PD++ M+K++ G +PL+ VV   + +D   PG   GT+ GN +A+AA  AV+  +
Sbjct: 289 HAGIIPDVVVMSKAIGGSLPLA-VVVYRDWLDTWLPGAHAGTFRGNQMAMAAGCAVMRYL 347

Query: 315 DKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDP-----QTGEPS-- 367
            +  +CE A  +G+RL   L   +   P +  +RG G M+ VE  DP       G P   
Sbjct: 348 VEHKVCEHAAAMGERLAEHLRILQRDFPQLGDIRGRGLMLGVELVDPTGALDAQGHPPAF 407

Query: 368 AAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420
           A +A  +Q+  L +GL+L   G +G V+RFL PL I  AQ D   +I   AL+
Sbjct: 408 ARLAPLVQRECLKRGLILELGGRHGAVVRFLPPLVITAAQIDRVAEIFGRALA 460


Lambda     K      H
   0.319    0.134    0.388 

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: 464
Number of extensions: 21
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: 421
Length of database: 466
Length adjustment: 32
Effective length of query: 389
Effective length of database: 434
Effective search space:   168826
Effective search space used:   168826
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 (21.8 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