Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Btheta:353284 Length = 373 Score = 199 bits (506), Expect = 1e-55 Identities = 137/394 (34%), Positives = 212/394 (53%), Gaps = 38/394 (9%) Query: 30 RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPYQGYVT 89 + + +WD G Y D G AV++ GH HP ++ I+ Q+ + ++ + Sbjct: 16 KGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVIN-KLQQQ 74 Query: 90 LAERINALVPIQGLNKTALF--TTGAEAVENAIKIARAHTGRPGVIAFSGAFHGRTLLGM 147 +AER+ I G +LF +GAEA ENA+K+A + GR VI+FS AFHGRT L + Sbjct: 75 VAERLGK---ISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHGRTSLAV 131 Query: 148 ALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPARVAAIIVE 207 T P+ I AP + +G T L +E + K ++ V A+I+E Sbjct: 132 EATNN-----------PTII--APINN--NGHVTYLPLNDIEAM-KQELAKGDVCAVIIE 175 Query: 208 PVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVEPDLITM 267 +QG GG + +FM+ LR VC + G +LI DE+Q+G+GR+GK FA ++ ++PD+IT+ Sbjct: 176 GIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITV 235 Query: 268 AKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEKLCERSAS 327 AK + G P++ V + M P+ G LG T+ GN LA +AA AV+DVIE++ L E + + Sbjct: 236 AKGIGNGFPMAGV--LISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKA 293 Query: 328 LGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQTRALEAGLVL 387 +G ++LL + K P + EVRG G M+ EF +P K +++R + V Sbjct: 294 VG----DYLLEELKKFPQIKEVRGRGLMIGLEFEEP---------IKELRSRLIYDEHV- 339 Query: 388 LTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421 T + NV+R L PL + + D LA + L Sbjct: 340 FTGASGTNVLRLLPPLCLSMEEADEFLARFKRVL 373 Lambda K H 0.321 0.136 0.400 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: 355 Number of extensions: 16 Number of successful extensions: 3 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: 423 Length of database: 373 Length adjustment: 31 Effective length of query: 392 Effective length of database: 342 Effective search space: 134064 Effective search space used: 134064 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 (21.9 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