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.
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:
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