Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate GFF305 Psest_0306 adenosylmethionine-8-amino-7-oxononanoate transaminase
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__psRCH2:GFF305 Length = 467 Score = 215 bits (548), Expect = 2e-60 Identities = 136/437 (31%), Positives = 217/437 (49%), Gaps = 14/437 (3%) Query: 18 HHLAPFSDFKQLKEKGPRI-ITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAA 76 H D +QL P I I GV+L D +G + LD ++ W G+ + Sbjct: 17 HPCTQMKDHEQL----PLIPIRRGDGVWLEDFDGKRYLDAVSSWWVNVFGHANPRINQRI 72 Query: 77 SKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYW 136 Q+ +L + L +H PV+EL++ + + P G++ VF+T +GS G + L+M HYW Sbjct: 73 KDQVDQLEHVMLA-GFSHQPVVELSERLVALTPAGLDRVFYTDNGSTGIEVALKMSFHYW 131 Query: 137 AIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDM 196 G+ K+ ++ N YHG TVA S+G + + + +P P + + Sbjct: 132 RNSGRGQKQRFVTLTNSYHGETVAAMSVGDVALFTDTYKPLLLDTFKVPSPDCYLRPDGV 191 Query: 197 TPEEFGIWAANQLEEKILELGVDTVGAFIAEP-IQGAGGVIIPPDSYWPRIKEILAKYDI 255 + EE +E+ + E D + A I EP IQGAGG+ + Y ++E +Y++ Sbjct: 192 SWEEHSRQMFAHMEQTLAEHHQD-IAAVIVEPLIQGAGGMRMYHPVYLKLLREACDRYEV 250 Query: 256 LFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGG 315 + DE+ GFGRTG F + G+ PD + ++K LT GY+PM ++ D + + + Sbjct: 251 HLIHDEIAVGFGRTGTMFACEQAGITPDFLCLSKALTGGYLPMAAVLTTDRIYQAFYDDY 310 Query: 316 D----FNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVG 371 F H TY+G+P+A A AL + I E+ +IE A + L DHP V Sbjct: 311 STLRAFLHSHTYTGNPLACAAALATLDIFAEDNVIE-ANKPLAARMASATAHLVDHPHVA 369 Query: 372 EVRGVGLLGAIELVQDKATRARYV-GKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVIT 430 EVR G+ AIE+VQDKA+R Y + G+ Q + G ++R +G + PP IT Sbjct: 370 EVRQTGMALAIEMVQDKASRTAYPWQERRGLKVYQHALERGALLRPLGSVVYFLPPYCIT 429 Query: 431 KAEIDELVTKARKCLDL 447 + +ID L A + +D+ Sbjct: 430 EEQIDFLAAVATEGIDI 446 Lambda K H 0.320 0.140 0.428 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: 505 Number of extensions: 29 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: 467 Length adjustment: 33 Effective length of query: 421 Effective length of database: 434 Effective search space: 182714 Effective search space used: 182714 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