GapMind for catabolism of small carbon sources

 

Aligments 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_4910 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= SwissProt::P50457
         (421 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910
           Acetylornithine aminotransferase (EC 2.6.1.11)
          Length = 413

 Score =  209 bits (531), Expect = 2e-58
 Identities = 132/385 (34%), Positives = 195/385 (50%), Gaps = 32/385 (8%)

Query: 34  LKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVTLAEKIN 93
           L D  G EY+D  AG+AV N GH HP +VAA+ +Q     HT+  +   +    LA+K+ 
Sbjct: 47  LWDQAGREYLDAVAGVAVTNVGHSHPKIVAAITEQAGLLLHTS-NLYSIDWQQRLAQKLT 105

Query: 94  ALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRPG-----VIAFSGGFHGRTYMTMALT 148
            LA   G  +  F  +GAEA E A+KIAR H    G     V+     FHGRT  T++ +
Sbjct: 106 QLA---GMDRAFFNNSGAEANETALKIARLHGWHKGIEQPLVVVMENAFHGRTLGTLSAS 162

Query: 149 GKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAIIFEPVQ 208
              A  ++GF   PG    VP+  DL       +LD +++ F S     ++ A++ EP+Q
Sbjct: 163 DGPA-VRLGFNKLPGDFVKVPF-GDL------GALDKVQQAFGS-----RIVAVLMEPIQ 209

Query: 209 GEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLMTMAKS 268
           GE G  +AP   ++A+R LC+    +++ DE+Q+G  RTG+ FA  H    PD+MT+AK 
Sbjct: 210 GESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 269

Query: 269 LAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCERANQLGQ 328
           L  G+P+   +      +   PG  G T+ GNPLA      VL+I++++ L E A   G 
Sbjct: 270 LGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLDIVEEQGLLENARLQGA 329

Query: 329 RLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQRALAQGLLLLTC 388
           RL   L       P ++ +RG G MI +E   P        I       A   GLL+   
Sbjct: 330 RLLERLRTELAGNPNVSQIRGQGLMIGIELKQP--------IRDLSLIAARDHGLLINV- 380

Query: 389 GAYGNVIRFLYPLTIPDAQFDAAMK 413
              GN IR L PLT+ + + +  ++
Sbjct: 381 -TRGNTIRLLPPLTLDEREVEMIVR 404


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: 414
Number of extensions: 22
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: 413
Length adjustment: 31
Effective length of query: 390
Effective length of database: 382
Effective search space:   148980
Effective search space used:   148980
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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