GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas fluorescens FW300-N2E3

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 AO353_15640 AO353_15640 acetylornithine aminotransferase

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_15640
          Length = 391

 Score =  196 bits (499), Expect = 8e-55
 Identities = 128/385 (33%), Positives = 193/385 (50%), Gaps = 32/385 (8%)

Query: 34  LKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVTLAEKIN 93
           L D  G EY+D  AG+AV N GH HP +V+A+ +Q     HT+  +   +    LA K+ 
Sbjct: 25  LWDQAGREYLDAVAGVAVTNVGHSHPKVVSAISEQAGLLLHTS-NLYSIDWQQRLAHKLT 83

Query: 94  ALAPVSGQAKTAFFTTGAEAVENAVKIARA---HTG--RPGVIAFSGGFHGRTYMTMALT 148
            L   SG  +  F  +GAEA E A+K+AR    H G  +P V+     FHGRT  T++ +
Sbjct: 84  QL---SGLDRVFFNNSGAEANETALKLARLYGWHKGVEQPLVVVMENAFHGRTLGTLSAS 140

Query: 149 GKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAIIFEPVQ 208
              A  ++GF   PG    VP+            L A+++  ++    +++ A++ EP+Q
Sbjct: 141 DGPA-VRLGFQELPGDFIKVPF----------GDLAALDKAHQT--HGQRIVAVLMEPIQ 187

Query: 209 GEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLMTMAKS 268
           GE G  +A    + A+R LC+    +++ DE+Q+G  RTG+ FA  H    PD+MT+AK 
Sbjct: 188 GESGVQLALPGYLKALRELCNRRNWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 247

Query: 269 LAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCERANQLGQ 328
           L  G+P+   +      +   PG  G T+ GNPLA      VL II+++ L E A + G+
Sbjct: 248 LGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLEIIEEQGLLENAKRQGE 307

Query: 329 RLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQRALAQGLLLLTC 388
           RL   L    +  P + A+RG G MI +E   P        I       A   GLL+   
Sbjct: 308 RLLARLHAELDGSPQVLAIRGQGLMIGIELARP--------IRDLTLIAARDHGLLINV- 358

Query: 389 GAYGNVIRFLYPLTIPDAQFDAAMK 413
              G  IR L PLTI + + +  ++
Sbjct: 359 -TRGKTIRLLPPLTIDEREVEMIVR 382


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: 381
Number of extensions: 24
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: 421
Length of database: 391
Length adjustment: 31
Effective length of query: 390
Effective length of database: 360
Effective search space:   140400
Effective search space used:   140400
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: 50 (23.9 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