GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Korea:Ga0059261_4131
          Length = 398

 Score =  196 bits (497), Expect = 1e-54
 Identities = 135/403 (33%), Positives = 195/403 (48%), Gaps = 44/403 (10%)

Query: 24  PIFADRAENCRVWDVEGRE-YLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSH--TCFQV 80
           PI  DR E   ++ V+G E YLD   G+A    GH HP +VAA+EAQ  KL H    F++
Sbjct: 13  PIAFDRGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISNMFEM 72

Query: 81  LAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAF 134
                  E      +     FA       +G+EAVE A+K+AR         +R   I F
Sbjct: 73  PGQNALAE------RLTTASFADTVFFTNSGTEAVECAIKVARRYHAARGEPQRQTVIGF 126

Query: 135 SGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKND 194
           SGA+HGRT+  +   G           +PG V+ A+   P   ++  D+           
Sbjct: 127 SGAFHGRTYGAMNAAGNPAHLDGFGDRLPGFVHFAVDNWPALALAIADSAT--------- 177

Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254
                 AA+V+EPVQGEGG  A +  F+ +LRA C  HG++LI DEVQ+G GRTG LFA 
Sbjct: 178 ------AAVVVEPVQGEGGARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKLFAH 231

Query: 255 E-QMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLK 313
           +      PD+   AK++  GFP+      AE    + PG  G T  GNP+A   A+    
Sbjct: 232 QWYPDATPDIMALAKALGSGFPVGACLATAEAASGMVPGVHGTTAGGNPLAMAVAIAAFD 291

Query: 314 VFEQENLLQKANDLGQKLKDGLLAIAEKHP-EIGDVRGLGAMIAIELFEDGDHNKPDAKL 372
              +   L  A ++ Q L+ GL  +A  HP  I ++RG G ++ + L  +          
Sbjct: 292 EIAKPETLTHAREVAQHLRAGLDRLAATHPGVISEIRGKGLLVGVRLVPN---------- 341

Query: 373 TAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415
               +A AR++ L++   G   N +R+L PLT+  A+  Q L+
Sbjct: 342 NRAFMAAAREQRLLVAGGGD--NCVRLLPPLTLTVAEADQILD 382


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: 441
Number of extensions: 32
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: 426
Length of database: 398
Length adjustment: 31
Effective length of query: 395
Effective length of database: 367
Effective search space:   144965
Effective search space used:   144965
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