GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Synechococcus elongatus PCC 7942

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 Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase

Query= SwissProt::P22256
         (426 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0943 Synpcc7942_0943
           acetylornithine aminotransferase
          Length = 422

 Score =  208 bits (530), Expect = 2e-58
 Identities = 134/401 (33%), Positives = 206/401 (51%), Gaps = 36/401 (8%)

Query: 24  PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAY 83
           P+  +R E CRVWD +GR YLDF  GIA    GH HP++V A+  Q++KL H     L Y
Sbjct: 35  PLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHHV--SNLYY 92

Query: 84  EPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTI---------AF 134
            P  E  ++         A +     +G+EA E A+K+AR   K   T+           
Sbjct: 93  IP--EQGQLAAWLTANSCADRVFFCNSGAEANEAAIKLAR---KHGNTVLEAENPIILTA 147

Query: 135 SGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKND 194
             ++HGRT   +  TG+   +     L+ G  Y          +  +D  A    + + D
Sbjct: 148 QASFHGRTLAAVTATGQPKYHKGFQPLVQGFRY----------VPYNDLAALEATLAELD 197

Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254
           AA E +AAI++EP+QGEGG      A+ Q +R LCD+  ++LI DEVQ G GR+G L+  
Sbjct: 198 AAGETVAAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLWGY 257

Query: 255 EQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKV 314
           E +G+ PD  T AK + GG P+  +  +A   + +  G    T+ GNP+AC A L + +V
Sbjct: 258 ENLGIEPDAFTVAKGLGGGVPIGALLVKAS-CNILQAGEHASTFGGNPLACRAGLAIAQV 316

Query: 315 FEQENLLQKANDLGQKLKDGLLAIAEKHPE-IGDVRGLGAMIAIELFEDGDHNKPDAKLT 373
            E++ LL      G++L+ GL  + +++P  +  VRG G +  + L      N P+    
Sbjct: 317 MERDQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLINGLVL-----RNDPNVTPI 371

Query: 374 AEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGL 414
           A +V  A ++GL+L+  G    V+R + PL +  A+I + L
Sbjct: 372 A-LVKAAIEQGLLLVPAGA--EVVRFVPPLIVSAAEIDEAL 409


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: 490
Number of extensions: 25
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: 426
Length of database: 422
Length adjustment: 32
Effective length of query: 394
Effective length of database: 390
Effective search space:   153660
Effective search space used:   153660
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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