GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Desulfovibrio vulgaris Hildenborough

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 208688 DVU3168 glutamate-1-semialdehyde-2,1-aminomutase

Query= SwissProt::P50457
         (421 letters)



>MicrobesOnline__882:208688
          Length = 423

 Score =  141 bits (355), Expect = 4e-38
 Identities = 123/402 (30%), Positives = 179/402 (44%), Gaps = 28/402 (6%)

Query: 25  FAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYES 84
           F   A  + L  V+G  +IDF      +  GH HP++ AAV   + + T       P E 
Sbjct: 36  FIARAAGSRLHTVDGETFIDFVESWGPMLLGHTHPEVTAAVHAAVDRGTSYG---APCED 92

Query: 85  YVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMT 144
            V LA K+    P  G        +G EA  +A+++AR +TGR  ++ F G +HG     
Sbjct: 93  EVVLAAKVVDALP--GVDMVRMVNSGTEATMSALRLARGYTGRTKLVKFVGCYHGHADPF 150

Query: 145 MALTGK-VAPYKIGFGP-FPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAAI 202
           +A  G  VA   I   P  P S            ++  + L A++ LF   +  K +AAI
Sbjct: 151 LASAGSGVATLSIPGTPGVPESTVRDTL------LAPYNDLAAVKDLFA--LHGKDIAAI 202

Query: 203 IFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDL 262
           I E V G  G        +  +R LCD+HG ++I DEV +GF R     A   +   PDL
Sbjct: 203 IVEAVAGNMGLVPPKAGFLEGLRELCDQHGALLIFDEVITGF-RVSFGGAQQRFGITPDL 261

Query: 263 MTMAKSLAGGMPLSGVVGNANIMDAPAPGG---LGGTYAGNPLAVAAAHAVLNIIDKESL 319
            T+ K + GG+P+    G   IM   AP G     GT +GNPLA+AA  A L+++ +   
Sbjct: 262 TTLGKIIGGGLPVGAYGGKREIMQRIAPCGEVYQAGTLSGNPLAMAAGIATLDVLSRSDY 321

Query: 320 CERANQLGQRLKNTLIDAK-ESVPAIAAVRGLGSMIAVEF-NDPQTGEPSA-----AIAQ 372
                ++   +K      K + VP    +  L SM  V F NDP T   SA     A+  
Sbjct: 322 AGLEARVAAFVKELEAILKGKGVP--VRINTLASMFTVFFTNDPVTDFASAKTADGALYT 379

Query: 373 KIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKI 414
              ++  AQG+ L        ++ F +      A  DAA K+
Sbjct: 380 SFYKQMRAQGIYLAPSPFEAAMVSFAHTDDDLAAMLDAARKV 421


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: 440
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: 423
Length adjustment: 32
Effective length of query: 389
Effective length of database: 391
Effective search space:   152099
Effective search space used:   152099
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