Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__Miya:8499751 Length = 459 Score = 245 bits (625), Expect = 2e-69 Identities = 156/440 (35%), Positives = 225/440 (51%), Gaps = 19/440 (4%) Query: 18 HHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAG-LWCVAIGYGRDELADAA 76 HHL F KGP I+ +G+ L D G + LD +G +WCV +GYGR+ +A A Sbjct: 22 HHLVQHQAFAG---KGPMIVVEGEGLTLRDINGKEYLDATSGGVWCVNVGYGRERIARAV 78 Query: 77 SKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYW 136 +QM+ +PYY + P +E A+ + P G+ + + SGSE N+ +MVR Sbjct: 79 YEQMKAMPYYAA--TAGNIPYIEFAQKLLAHMP-GLTRAYLSNSGSEANEKAYKMVRSLA 135 Query: 137 AIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDM 196 + G P KK I+ R YHG+T+ S G E +PG V P + + Sbjct: 136 HLSGNPAKKKILFRARDYHGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNK 195 Query: 197 TPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDIL 256 T I A +E I + G +TVG I EPI GGVI P Y+ + +I ++ +L Sbjct: 196 TYPGCDIDCARAVERIIEQEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVL 255 Query: 257 FVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEV-LNEGG 315 + DEV+CG GRTG FG YG+ PD++T+AKG+ S Y+P+ +EV + LN+ Sbjct: 256 LIMDEVVCGMGRTGTMFGYQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPA 315 Query: 316 D----FNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVG 371 D F TY G + ALEN+ I+ EEK++++V A YL L+EL D P VG Sbjct: 316 DKMAYFRDISTYGGCAAGCSAALENMAIIEEEKLLDNVNA-MGDYLLAGLKELGDLPYVG 374 Query: 372 EVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMR------AVGDTMIIAP 425 +VRG GLL IELVQDKA + V + + + L+ R + + IAP Sbjct: 375 DVRGKGLLCGIELVQDKAGKKPMAEGKVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAP 434 Query: 426 PLVITKAEIDELVTKARKCL 445 V+T+ ID ++ R L Sbjct: 435 AYVVTRDNIDVILRTLRAAL 454 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: 546 Number of extensions: 35 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: 459 Length adjustment: 33 Effective length of query: 421 Effective length of database: 426 Effective search space: 179346 Effective search space used: 179346 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