Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate SMc01534 SMc01534 omega amino acid--pyruvate transaminase
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__Smeli:SMc01534 Length = 442 Score = 295 bits (754), Expect = 3e-84 Identities = 168/431 (38%), Positives = 243/431 (56%), Gaps = 17/431 (3%) Query: 22 PFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMR 81 PF+ +Q K K PR+ AK +Y +G +LDG AGLWCV G+ R ++ +A +Q Sbjct: 18 PFTANRQFK-KEPRLFVGAKDMYYTTHDGRTVLDGTAGLWCVNAGHCRPKITEAIREQAG 76 Query: 82 ELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQ 141 EL Y F Q HP ELA + DIAPEGMNHV +T SGSE DT L++ Y KG Sbjct: 77 ELDYAPAF-QLGHPKAFELANRLVDIAPEGMNHVLYTNSGSESVDTALKVALAYHRAKGN 135 Query: 142 PNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMTPE-E 200 ++ +I R GYHG G S+GG+ + + G+ H+P + + E E Sbjct: 136 GSRFRLIGRERGYHGVNFGGISVGGIVANRKMFGTLLTGVDHLPHTHLPAKNAFSRGEPE 195 Query: 201 FGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVAD 260 G A +LE + TV A I EP+ G+ GV+IPP Y +++EI K+ IL + D Sbjct: 196 HGADLAAELERIVTLHDASTVAAVIVEPVAGSTGVLIPPKGYLQKLREICTKHGILLIFD 255 Query: 261 EVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGG----D 316 EVI G+GR G F + ++ +KPD++T AKGLT+G IPMG + V E+ + G + Sbjct: 256 EVITGYGRLGTPFAAQYFDVKPDIITTAKGLTNGVIPMGAVFVTSEIHDAFMTGPEHLIE 315 Query: 317 FNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVGEVRGV 376 F HG+TYSG+P+A+A AL + REE ++ AE APY ++ L L D P V ++R + Sbjct: 316 FFHGYTYSGNPIASAAALGTLDTYREEGLLTRA-AELAPYWEEALHSLKDCPHVIDIRNI 374 Query: 377 GLLGAIEL--VQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVITKAEI 434 GL+GA+EL + + T+ + ++ GL++R GD + ++PPL+I K +I Sbjct: 375 GLIGAVELEPIAGEPTKRAF-------SAFLKAYEKGLLIRTTGDIIALSPPLIIEKRQI 427 Query: 435 DELVTKARKCL 445 DEL K R L Sbjct: 428 DELFDKLRDVL 438 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: 543 Number of extensions: 37 Number of successful extensions: 6 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: 442 Length adjustment: 33 Effective length of query: 421 Effective length of database: 409 Effective search space: 172189 Effective search space used: 172189 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