GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas putida KT2440

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 PP_4223 PP_4223 diaminobutyrate-2-oxoglutarate transaminase

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__Putida:PP_4223
          Length = 452

 Score =  218 bits (556), Expect = 2e-61
 Identities = 146/403 (36%), Positives = 216/403 (53%), Gaps = 27/403 (6%)

Query: 29  AENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFT--HTAYQIVPYESYV 86
           A    ++DVEG ++ID  AG   L  GH HP +V A+++ L      HT     P +   
Sbjct: 38  ARGIHVEDVEGRQFIDCLAGAGTLALGHNHPVVVEAIQRVLADELPLHTLDLTTPVKD-- 95

Query: 87  TLAEKINALAP--VSGQAKTAFF-TTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYM 143
              + +  + P  +  +AK  F   TG +AVE A+K+ R  TGR  V+AF G +HG +  
Sbjct: 96  RFVQDLFGILPEALRREAKVQFCGPTGTDAVEAALKLVRTATGRSTVLAFQGAYHGMSQG 155

Query: 144 TMALTGKVAPYKIGFGPFPGS-VYHVPYPSDLH---GISTQDSLDA----IERLFKSDIE 195
            + L G   P K   G   G+ V  +PYP D     G+  +  + A    +E L      
Sbjct: 156 ALNLMGSHGP-KQPLGALLGNGVQFMPYPYDYRCPFGLGGEAGVKANLHYLENLLLDPES 214

Query: 196 AKQV-AAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMD 254
              + AA+I E VQGEGG   A  E +  +RR+ ++ G+ +I DE+QSGFARTG++FA +
Sbjct: 215 GVPLPAAVILEVVQGEGGVVPADIEWLKGVRRITEQAGVALIVDEIQSGFARTGRMFAFE 274

Query: 255 HYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNII 314
           H    PD++T++K++ G +PL+ VV   + +D   PG   GT+ GN +A+AA  AV+N +
Sbjct: 275 HAGIVPDVVTLSKAIGGSLPLA-VVVYRDWLDTWKPGAHAGTFRGNQMAMAAGSAVINYL 333

Query: 315 DKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAA----- 369
            +  L E A  +GQRL+  L   +   P +  +RG G M+ VE  DPQ G+P A      
Sbjct: 334 VEHRLAEHAEAMGQRLRGHLQRLQRDYPQLGDIRGRGLMLGVELVDPQ-GQPDALGHPPA 392

Query: 370 ---IAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFD 409
              +A K+Q+  L +GL+L   G +G V+RFL PL I   Q D
Sbjct: 393 NRDLAPKVQRECLKRGLILELGGRHGAVVRFLPPLIISAEQID 435


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: 504
Number of extensions: 27
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: 421
Length of database: 452
Length adjustment: 32
Effective length of query: 389
Effective length of database: 420
Effective search space:   163380
Effective search space used:   163380
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