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_066608605.1 V473_RS18720 diaminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_001046645.1:WP_066608605.1
          Length = 436

 Score =  181 bits (459), Expect = 4e-50
 Identities = 134/418 (32%), Positives = 206/418 (49%), Gaps = 19/418 (4%)

Query: 7   LMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAV 66
           + +RR  A+ R   +  P   ++A+   + D +G  YLDF  G + LN GH HP +  A+
Sbjct: 18  IYERRESAV-RSYARAMPRQFNQAQGVWMHDNQGGRYLDFLSGCSTLNYGHNHPVLKNAL 76

Query: 67  EAQLKKLSHTCFQVLAYEPYLELCEIMNQKV--PGDFAKKTLLV-TTGSEAVENAVKIAR 123
              +     T    L  +   +    +   +  P D   + +    TG+ AVE A+K+AR
Sbjct: 77  VDYIVNDGITHGLDLHTDAKADFLAALEDVILTPRDLDYRAMFTGPTGTNAVEAAIKLAR 136

Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDA 183
             T R   IAF+  +HG T   LA TG       G G+   HV    Y    HG   D A
Sbjct: 137 KITGRELVIAFTNGFHGMTLGALACTGNAAK-RGGAGVPLNHVSHEPYD-GYHGPGVDTA 194

Query: 184 IASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQS 243
                R+    +  +  AAI++E VQGEGG  A+SP +++++  +   HG ++I D++Q+
Sbjct: 195 EQLERRLSDPSSGLDAPAAILVETVQGEGGLNAASPRWLRQIADIAKRHGALMIIDDIQA 254

Query: 244 GAGRTGTLFAMEQMGVAPDLTTFAKSIAG-GFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           G GRTG  F+ E MG  PD+ T AKS++G G P A    R E +D  +PG   GT+ GN 
Sbjct: 255 GCGRTGNFFSFEGMGFTPDIVTMAKSLSGMGLPFALTLFRPE-LDQWSPGEHNGTFRGNN 313

Query: 303 IACVAALEVLKVFEQE-NLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFE 361
            A V A   L+ F  + N  Q     G  L+  L A+A +H     +RG G M  I++  
Sbjct: 314 HAFVTATATLRHFWSDGNFQQDIARRGALLERRLAAMATEHGL--SIRGRGMMRGIDV-- 369

Query: 362 DGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419
                    ++   I A    +GLI+ + G +  ++++L PL I+D+ +  GL+I+ Q
Sbjct: 370 ------GSGEIAQTITAACFAQGLIIETSGAHDEIVKVLAPLVIDDSVLSAGLDILEQ 421


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: 475
Number of extensions: 23
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: 436
Length adjustment: 32
Effective length of query: 394
Effective length of database: 404
Effective search space:   159176
Effective search space used:   159176
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 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