Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 3608649 Dshi_2042 aminotransferase class-III (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_13150 (454 letters) >FitnessBrowser__Dino:3608649 Length = 460 Score = 242 bits (618), Expect = 2e-68 Identities = 150/436 (34%), Positives = 230/436 (52%), Gaps = 28/436 (6%) Query: 18 HHLAPFSDFKQLKEKGPRIITHAKGVYLWDSEGNKILDGMAG-LWCVAVGYGREELADAA 76 HHL + K + PRII KG+ +WD+ G + LD ++G LW V VGYGRE +A+A Sbjct: 23 HHLI---NHKPFETTDPRIIVEGKGMRVWDALGKEHLDAVSGGLWTVNVGYGRERIANAV 79 Query: 77 SQQMRELPYYNLFFQTAHPPVLELSKAIADIAPEGMNHVFFTGSGSEGNDTMLRMVRHYW 136 Q+ ++ +++ T P S+ + D P GM+ V++ SGSE N+ +MVR Sbjct: 80 RDQLMQMCFFSNSLGTI--PGAIFSEMLIDKMP-GMSRVYYASSGSEANEKAFKMVRQIA 136 Query: 137 AIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIAQPYWFGEGGDM 196 K I+ R+ YHGST+A S GG Q P V + P+ Sbjct: 137 HKVHGGRKTKILYRERDYHGSTLATMSAGGQWERKAQYGPFAPDFVEV--PHCLEYRAQW 194 Query: 197 SPEEFGVWAANQLEEKILEIGVDNVGAFIAEPIQGAGGVIVPPDSYWPRMKEILAKYDIL 256 E +G AA+ +EE IL G D VGA EP+ GGVI PP+ YWPR++EI KYD+L Sbjct: 195 EGENYGERAADAIEEVILREGPDTVGALCLEPVTAGGGVITPPEGYWPRVQEICRKYDVL 254 Query: 257 FVADEVICGFGRTGEWFGTDHYGLKPHMMTIAKGLTSGYIPMGGLIVRDDVVAVL-NEGG 315 DEV+CG GRTG+WFG HYG++P +T+AKG+ SGY + ++ + V + +E G Sbjct: 255 LHIDEVVCGLGRTGKWFGYQHYGIEPDFVTMAKGVASGYAAISCMVTTERVFEMFKSEPG 314 Query: 316 D----FNHGFTYSGHPVAAAVALENIRILRDEKII---ERVHSETAPYLQKRLRELNDHP 368 F T+ G A A+EN++I+ +E ++ +R+H + L + + H Sbjct: 315 APLDYFRDISTFGGCTAGPAAAIENMKIIEEEDLLGNTDRMHDQLMGNLAGLMEK---HR 371 Query: 369 LVGEVRGVGLLGAIELVQDKATRKRYEGKGVGMICRQFCFDNGLIMRAV-------GDTM 421 ++G++RG GL ELV D+ T++ V + C G+I+ A +T+ Sbjct: 372 VIGDIRGKGLFCGAELVADRTTKEPAPEALVQAVVAD-CMAQGVIIGATNRSLPGYNNTL 430 Query: 422 IIAPPLVISKAEIDEL 437 +P L+ + +ID++ Sbjct: 431 CFSPALIATADDIDQI 446 Lambda K H 0.320 0.139 0.431 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: 593 Number of extensions: 34 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: 454 Length of database: 460 Length adjustment: 33 Effective length of query: 421 Effective length of database: 427 Effective search space: 179767 Effective search space used: 179767 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 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