GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_205 Pyoverdin biosynthesis protein PvdH, L-2,4-diaminobutyrate:2-oxoglutarate aminotransferase (EC 2.6.1.76)

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_205
          Length = 470

 Score =  227 bits (578), Expect = 7e-64
 Identities = 145/412 (35%), Positives = 218/412 (52%), Gaps = 23/412 (5%)

Query: 29  AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFT--HTAYQIVPYESYV 86
           A+   ++DVEG  +ID  AG   L  GH HP ++ A++Q L      HT     P +   
Sbjct: 56  AKGIYVEDVEGRSFIDCLAGAGTLALGHNHPVVIEAIQQVLTDELPLHTLDLTTPVKDQF 115

Query: 87  TLAEKINALAP-VSGQAKTAFF-TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMT 144
            + +    L P ++ +AK  F   TG +AVE A+K+ R  TGR  V++F GG+HG +   
Sbjct: 116 -VQDLFGLLPPALAAEAKIQFCGPTGTDAVEAALKLVRTATGRSTVLSFQGGYHGMSQGA 174

Query: 145 MALTGKVAPYKIGFGPFPGSVYHVPYPSDLH-------GISTQDSLDAIERLFKSDIEAK 197
           ++L G + P K         V  +PYP D             Q +L+ +E L        
Sbjct: 175 LSLMGSLGPKKPLGALLSSGVQFMPYPYDYRCPFGLGGAQGVQVNLNYLENLLNDPEAGV 234

Query: 198 QV-AAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHY 256
           Q+ AA+I E VQGEGG   A  + +  +RR+ ++ G+ +I DE+QSGFARTGK+FA +H 
Sbjct: 235 QLPAAVIVEAVQGEGGVIPADLDWLRGLRRITEKAGVALIVDEIQSGFARTGKMFAFEHA 294

Query: 257 ADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDK 316
              PD++ M+K++ G +PL+ VV   + +D   PG   GT+ GN +A+AA  AV+  + +
Sbjct: 295 GIIPDVVVMSKAIGGSLPLA-VVVYRDWLDTWLPGAHAGTFRGNQMAMAAGSAVMRYLTE 353

Query: 317 ESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPS--------A 368
             +CE A  +G+RL   L   +   P +  +RG G M+ VE  DP TG P         A
Sbjct: 354 HKVCEHAAAMGERLSEHLHILQRDFPQLGDIRGRGLMLGVELVDP-TGAPDAQGHPPIFA 412

Query: 369 AIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420
            +A  +Q+  L +GL+L   G +G V+RFL PL I  A+ D    I   A++
Sbjct: 413 RLAPLVQRECLKRGLILELGGRHGGVVRFLPPLVITAAEIDRVADIFGRAMA 464


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: 480
Number of extensions: 23
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: 470
Length adjustment: 32
Effective length of query: 389
Effective length of database: 438
Effective search space:   170382
Effective search space used:   170382
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