GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Caulobacter crescentus NA1000

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 CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Caulo:CCNA_00620
          Length = 392

 Score =  193 bits (491), Expect = 7e-54
 Identities = 129/393 (32%), Positives = 199/393 (50%), Gaps = 43/393 (10%)

Query: 29  RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTC--FQVLAYEPY 86
           R E C ++D +GR+YLD A G+AV   GH  P++V A++ Q   L H    +++ A E  
Sbjct: 17  RGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWHASNLYRLPAQEA- 75

Query: 87  LELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAFSGAYHG 140
                +  +     FA +     +G+EAVE A+K AR         +R   + F  A+HG
Sbjct: 76  -----LATKLTDATFADRVFFANSGAEAVEAAIKTARRWQGAKGRPERYRVLTFGNAFHG 130

Query: 141 RTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPEDI 200
           RT  T++ T ++       G  P  +Y A    P + I  + A  +I             
Sbjct: 131 RTLATISATDQMKVRE---GFTP--LYDAFDTTPFNDI--EGAARAI---------TPQT 174

Query: 201 AAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQMGVA 260
           AAI++EP+QGEGG   ++P F+  LRALCD+H ++LI DEVQ+G GRTG LFA E  GV 
Sbjct: 175 AAILVEPIQGEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHELYGVR 234

Query: 261 PDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENL 320
           PD+   AK + GGFP+       +    + PG  G TY GNP+AC  A  VL        
Sbjct: 235 PDIIAVAKGLGGGFPIGACLATEDAASGMTPGSHGSTYGGNPLACAVASAVLDAVLAPGF 294

Query: 321 LQKANDLGQKLKDGLLAIAEKHPEI-GDVRGLGAMIAIELFEDGDHNKPDAKLTAEIVAR 379
           L+   +    +   L  +  +H ++    +G G M  +++       +  A+   ++VA 
Sbjct: 295 LETVRERAALVDALLERLLRRHSDLFVRAQGHGLMRGLQV-------RASAR---DVVAH 344

Query: 380 ARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQ 412
            RD G++ ++ G   +V+R+L PLTI + +I +
Sbjct: 345 LRDFGVMTVAAGA--DVVRLLPPLTISELEIAE 375


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: 393
Number of extensions: 21
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: 392
Length adjustment: 31
Effective length of query: 395
Effective length of database: 361
Effective search space:   142595
Effective search space used:   142595
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