Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Echvi_0124 Echvi_0124 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >FitnessBrowser__Cola:Echvi_0124 Length = 386 Score = 264 bits (674), Expect = 4e-75 Identities = 137/381 (35%), Positives = 213/381 (55%), Gaps = 2/381 (0%) Query: 6 ITPADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPK 65 I PA R+ + Y F++ A+ + +G +I++G+G+PD V +A + P Sbjct: 2 IAPAHRLANVKEYYFSKKLREVARLKAEGHPIINMGIGSPDLPPHPSVTEALNHSSAQPT 61 Query: 66 NHGYPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVL 125 +HGY ++G + R AI ++Y + Y V L P E LP++GSKE + H+++AY+NPGD VL Sbjct: 62 SHGYQSYQGIPALREAIASFYQKHYAVSLSPTDEILPMMGSKEAIMHISLAYLNPGDKVL 121 Query: 126 VPSPAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGA 185 +P+P YP + + G LK EN WL D+ + E K+++ NYP PTGA Sbjct: 122 IPNPGYPTYSSVTELVGAKAVYYDLKEENQWLPDIGQLEELAQSGIKLMWINYPHMPTGA 181 Query: 186 TAPREFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTY 245 A RE E +V FA+K++ILLV+D Y+ + P S+L I GAKDI +E ++LSKT+ Sbjct: 182 NASREALEALVTFAKKHQILLVNDNPYSFILTQ--SPISILSIDGAKDIALELNSLSKTF 239 Query: 246 NMAGWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTR 305 NM GWRVG + G +Q + +K+N+D G+F +Q A AL L + ++ Y R Sbjct: 240 NMPGWRVGMLCGQASYLQEVLKVKSNMDSGMFLGIQEGAIAALNLDQRWFDQMDAIYHKR 299 Query: 306 RDFLIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGE 365 R+ + + +G + A M++W K + LL + + +TPG+ FG G Sbjct: 300 REAVWKLAERVGAICERNSAGMFVWAKLATQTTPSALVDKLLYENHIFITPGDIFGSNGH 359 Query: 366 GYVRISLIADCDRLGEALDRI 386 GY+R SL + + EA DR+ Sbjct: 360 GYIRFSLCVPENLIQEAFDRV 380 Lambda K H 0.321 0.140 0.427 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: 410 Number of extensions: 16 Number of successful extensions: 2 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: 403 Length of database: 386 Length adjustment: 31 Effective length of query: 372 Effective length of database: 355 Effective search space: 132060 Effective search space used: 132060 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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