Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 3607958 Dshi_1366 aminotransferase class-III (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_08585 (454 letters) >FitnessBrowser__Dino:3607958 Length = 441 Score = 270 bits (690), Expect = 7e-77 Identities = 151/425 (35%), Positives = 232/425 (54%), Gaps = 20/425 (4%) Query: 22 PFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASKQMR 81 PF+ +Q K PR+ A G+Y +EG ++LDG AGLWC G+ R + +A Q Sbjct: 18 PFTANRQFKSN-PRMFVAADGMYYTTAEGRQVLDGTAGLWCCNAGHKRPRIVEAIQAQAA 76 Query: 82 ELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYWAIKGQ 141 EL Y F Q HP ELA + +IAP+GM+HVF+T SGSE ++ L++ Y +G+ Sbjct: 77 ELDYAPAF-QMGHPRAFELANRLVEIAPDGMDHVFYTNSGSEAVESALKIALAYHRARGE 135 Query: 142 PNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMTPEEF 201 + +I R GYHG G S+GG+ + + G+ H+P + E Sbjct: 136 AGRTRLIGRERGYHGVNFGGISVGGIVNNRKHFGTLLTGVDHLPHTHIPENQWSRGMPEL 195 Query: 202 GIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEILAKYDILFVADE 261 G A+ LE I G +T+ A I EP+ G+ GV++PP Y R+++I + I+ + DE Sbjct: 196 GAHLADDLERIIALHGAETIAAVIVEPMAGSTGVLLPPKGYLQRLRKITQDHGIVLIFDE 255 Query: 262 VICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGG----DF 317 VI GFGR G FG+ +G+ PDM+T AKGLT+G IPMG ++ + + +G + Sbjct: 256 VITGFGRVGAAFGAQRFGVTPDMITCAKGLTNGVIPMGAVLCGSHIHDAFMQGPENLIEL 315 Query: 318 NHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVGEVRGVG 377 HG+TYSG+P+A+A L + RE+ + + PY Q+ L L V ++R +G Sbjct: 316 FHGYTYSGNPIASAAGLATLETYREDDLFARA-LDLEPYWQEALHSLKGARHVIDIRNLG 374 Query: 378 LLGAIEL--VQDKATRARYVGKGVGMICRQF--CFDNGLIMRAVGDTMIIAPPLVITKAE 433 L+GAIEL + T+ + + F +D G+++R GD + ++PPL+I A+ Sbjct: 375 LIGAIELEPISGHPTKRAF---------QAFLDAYDKGVLIRTTGDIIALSPPLIIETAQ 425 Query: 434 IDELV 438 ID +V Sbjct: 426 IDRIV 430 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: 550 Number of extensions: 31 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: 441 Length adjustment: 33 Effective length of query: 421 Effective length of database: 408 Effective search space: 171768 Effective search space used: 171768 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