GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Escherichia coli BW25113

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 17148 b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__Keio:17148
          Length = 459

 Score =  198 bits (503), Expect = 3e-55
 Identities = 141/403 (34%), Positives = 217/403 (53%), Gaps = 30/403 (7%)

Query: 27  QSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQL-QQFTHTAYQIVPYESY 85
           Q+    TL D +G E+ID   G  + N GHR+P +V+AV+ QL +Q  H+   + P  + 
Sbjct: 69  QAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM 128

Query: 86  VTLAEKINALAPVSGQAKTAFF-TTGAEAVENAVKIARAHTGRPG---VIAFSGGFHGRT 141
             LA+ + AL P  G+ K +FF  +G E+VE A+K+A+A+    G    IA SG FHG++
Sbjct: 129 --LAKTLAALTP--GKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKS 184

Query: 142 YMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIEAKQVAA 201
              ++ T K + ++  F P      HVP+  ++  + T     A+    K+      VAA
Sbjct: 185 LGALSATAK-STFRKPFMPLLPGFRHVPF-GNIEAMRT-----ALNECKKT---GDDVAA 234

Query: 202 IIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPD 261
           +I EP+QGEGG  + P   + A+R+LCDE G +MI DEVQ+G  RTGK+FA +H   +PD
Sbjct: 235 VILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPD 294

Query: 262 LMTMAKSLAGG-MPLSGVVGNANIMDA--PAPGGLGGTYAGNPLAVAAAHAVLNIIDKES 318
           ++ +AK+L GG MP+   +    +       P     T+ GNPLA AAA A +N++ +++
Sbjct: 295 ILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQN 354

Query: 319 LCERANQLGQRLKNTLID-AKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQR 377
           L  +A Q G  L +     A+E    +   RG G ++A+EF D + G   A  ++  +QR
Sbjct: 355 LPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFA--SEMFRQR 412

Query: 378 ALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420
            L  G L          IR   PLT+   Q +  +K  + AL+
Sbjct: 413 VLVAGTL-----NNAKTIRIEPPLTLTIEQCELVIKAARKALA 450


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: 439
Number of extensions: 21
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: 459
Length adjustment: 32
Effective length of query: 389
Effective length of database: 427
Effective search space:   166103
Effective search space used:   166103
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