GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Dyadobacter tibetensis Y620-1

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 WP_025761698.1 X939_RS0102485 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000566685.1:WP_025761698.1
          Length = 405

 Score =  189 bits (481), Expect = 1e-52
 Identities = 135/416 (32%), Positives = 198/416 (47%), Gaps = 60/416 (14%)

Query: 29  RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88
           RAE   ++D EG+ Y+D   GI V N GH HPKV+ A+  QL K  H    +L Y  +++
Sbjct: 27  RAEGLYMYDQEGKSYMDLISGIGVSNVGHRHPKVLKAIYDQLDKHMH----LLVYGEFIQ 82

Query: 89  LCEIM-------------NQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFS 135
             +++              +  P        L  +G+EAVE A+K+A+  T R+  IA  
Sbjct: 83  SSQVLLAQALANTLTLPEERSAPYGAIDHIYLTNSGTEAVEGAMKLAKRYTGRNEFIACY 142

Query: 136 GAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGIS--EDDAIASIHRIFKN 193
            AYHG T   L+L G                ++  Y   L GIS  E  A+A + RI   
Sbjct: 143 NAYHGATQGALSLAG-------------AEFFKNSYRPLLPGISHIEHGALADLSRI--- 186

Query: 194 DAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFA 253
               E  AAI+IE V GE G       + + LR  C E G +LI DE+Q+G GRTG+ +A
Sbjct: 187 ---TEKTAAIIIEIVGGEAGVRIPPSGYFEALRQRCTETGTLLILDEIQTGYGRTGSFWA 243

Query: 254 MEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGG---TYAGNPIACVAALE 310
            EQ  + PD+   AK + GG P+        +M       + G   T+ G+P++  AAL 
Sbjct: 244 FEQYNIYPDILLSAKGMGGGMPIGAFMASQTIMQVFKDNPVLGHITTFGGHPVSAAAALA 303

Query: 311 VLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDA 370
            L V  +E L +KA + G   K+ L     +HP I +VRG G M+A+E+           
Sbjct: 304 ALNVTLEERLAEKAIEKGALFKELL-----RHPRIKEVRGKGLMLAVEM--------ESF 350

Query: 371 KLTAEIVARARDKGLI---LLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDE 423
            +    +    D+G++    L C    N +RI  PL IE+ +IR   +II +  D+
Sbjct: 351 SILKRTIDLCIDQGIVTDWFLFCD---NAMRIAPPLIIEEKEIRLACDIILKAMDQ 403


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: 418
Number of extensions: 27
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: 405
Length adjustment: 31
Effective length of query: 395
Effective length of database: 374
Effective search space:   147730
Effective search space used:   147730
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 24 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