GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Sphingobium czechense LL01

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_066600058.1 V473_RS02290 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_001046645.1:WP_066600058.1
          Length = 398

 Score =  207 bits (526), Expect = 6e-58
 Identities = 145/398 (36%), Positives = 194/398 (48%), Gaps = 38/398 (9%)

Query: 29  RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLE 88
           R E C +    G  YLDFA GIAV   GH HP++V A+  Q   L H     L   P  E
Sbjct: 19  RGEGCYLIGERGERYLDFASGIAVNLLGHGHPRLVKAIADQAATLMHV--SNLYGMPLGE 76

Query: 89  LCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAFSGAYHGRT 142
             +   + V   FA       +G+EAVE A+K AR          R   I+F  A+HGRT
Sbjct: 77  --QFAQKLVDNSFADTVFFTNSGAEAVECAIKTARRYHYANGQAHRHKIISFDNAFHGRT 134

Query: 143 HYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDIAA 202
             T++ T +         L+PG         P + +  D A+A I          ++ A 
Sbjct: 135 LGTISATSQPKMRDGFEPLLPGFTV-----VPFNDL--DAALAQID---------DNTAG 178

Query: 203 IVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVAPD 262
            ++EPVQGEGG   S+ AF++ LR  CD HG++LI DEVQ G  RTGT FA EQ GV PD
Sbjct: 179 FLLEPVQGEGGVTPSTQAFLKGLREACDAHGLLLILDEVQCGYARTGTFFAHEQYGVTPD 238

Query: 263 LTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLLQ 322
           +   AK I  GFPL       E    +  G  G TY GNP+A    + VL+    +  L 
Sbjct: 239 IMAVAKGIGAGFPLGACLATEEAAKGMVFGTHGSTYGGNPLAMAVGIAVLEEVLADGFLD 298

Query: 323 KANDLGQKLKDGLLAIAEKHPEI-GDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVARAR 381
           +   +G +L+  L  +   H  +  DVRG+G M+ ++L         DA      V   R
Sbjct: 299 RVTAMGARLRSALEQLIPNHDGMFEDVRGMGLMLGVKL--------KDAHDARAFVGHLR 350

Query: 382 D-KGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIIS 418
           D  GL+ +S G   NVLRIL PL IE++ I + +E IS
Sbjct: 351 DHHGLLAVSAG--QNVLRILPPLVIEESHIAECIEKIS 386


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: 468
Number of extensions: 18
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 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