GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Escherichia coli BW25113

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate 17422 b3359 bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase (NCBI)

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Keio:17422
          Length = 406

 Score =  234 bits (598), Expect = 3e-66
 Identities = 146/407 (35%), Positives = 218/407 (53%), Gaps = 42/407 (10%)

Query: 22  IHPIFAD------RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSH 75
           I PI+A       + +  R+WD +G+EY+DFAGGIAV   GH HP +V A++ Q + L H
Sbjct: 17  ILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWH 76

Query: 76  TCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR--AATKRSG--- 130
               V   EP L L   +   +   FA++ + + +G+EA E A K+AR  A  + S    
Sbjct: 77  IS-NVFTNEPALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKT 132

Query: 131 -TIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHR 189
             IAF  A+HGR+ +T+++ G+   YS G G  P  +       P + +    A+   H 
Sbjct: 133 KIIAFHNAFHGRSLFTVSVGGQPK-YSDGFGPKPADIIHV----PFNDLHAVKAVMDDHT 187

Query: 190 IFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTG 249
                       A+V+EP+QGEGG  A++P F+Q LR LCD+H  +L+ DEVQ G GRTG
Sbjct: 188 -----------CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTG 236

Query: 250 TLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAAL 309
            LFA    GV PD+ T AK++ GGFP++ +   AE+  A  PG  G TY GNP+AC  A 
Sbjct: 237 DLFAYMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAG 296

Query: 310 EVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPD 369
               +     +L+      Q+  D L  I +++    D+RG+G +I  EL       KP 
Sbjct: 297 AAFDIINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL-------KPQ 349

Query: 370 AKLTA-EIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415
            K  A + +    + G+++L+ GP  +V+R    L +EDA I +G++
Sbjct: 350 YKGRARDFLYAGAEAGVMVLNAGP--DVMRFAPSLVVEDADIDEGMQ 394


Lambda     K      H
   0.320    0.137    0.401 

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: 474
Number of extensions: 20
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: 426
Length of database: 406
Length adjustment: 31
Effective length of query: 395
Effective length of database: 375
Effective search space:   148125
Effective search space used:   148125
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.

Links

Downloads

Related tools

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