Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate GFF1682 PS417_08560 aminotransferase
Query= curated2:P63499 (429 letters) >FitnessBrowser__WCS417:GFF1682 Length = 403 Score = 572 bits (1474), Expect = e-168 Identities = 279/403 (69%), Positives = 337/403 (83%), Gaps = 5/403 (1%) Query: 29 AQSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALPY 88 ++S KL +V Y+IRGPV +HA RLE EGHRILKLNIGNPAPFGFEAPD I++D+I+ LP Sbjct: 4 SKSNKLANVCYDIRGPVLKHAKRLEEEGHRILKLNIGNPAPFGFEAPDEILQDVIRNLPT 63 Query: 89 AQGYSDSQGILSARRAVVTRYEL--VPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQ 146 AQGYSDS+G+ SAR+AV+ Y+ V G ++D+YLGNGVSELI M++QALL+NGD+ Sbjct: 64 AQGYSDSKGLFSARKAVMQYYQQKQVEGV---GIEDIYLGNGVSELIVMSMQALLNNGDE 120 Query: 147 VLIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPT 206 VL+P+PDYPLWTA+ +LAGG PVHYLCDE W PD+AD+++KIT TKALV+INPNNPT Sbjct: 121 VLVPAPDYPLWTAAVTLAGGHPVHYLCDEGADWFPDLADIKAKITPNTKALVIINPNNPT 180 Query: 207 GAVYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKA 266 GAVYS E+L M++LAR+H L++ +DEIYDKILYDDA H+ AS+APD+LCLTFNGLSK+ Sbjct: 181 GAVYSREVLLGMLELARQHNLVVFSDEIYDKILYDDAVHVCTASLAPDLLCLTFNGLSKS 240 Query: 267 YRVAGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVL 326 YRVAG+R+GW+AI+GPK +A S+IEGI +LANMRLC NVP+QHAIQ ALGG+QSI DLVL Sbjct: 241 YRVAGFRSGWIAISGPKHNAQSYIEGIDILANMRLCANVPSQHAIQTALGGYQSINDLVL 300 Query: 327 PGGRLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKI 386 P GRLLEQR+ W LN IPGVSCVKP GALYAFPR+DP+V I +DE+ VLDLLLSEK+ Sbjct: 301 PQGRLLEQRNRTWELLNAIPGVSCVKPMGALYAFPRIDPKVCPILNDEKFVLDLLLSEKL 360 Query: 387 LVTQGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429 LV QGT FNWP PDH R+VTLP DL AI R+GNFL SYRQ Sbjct: 361 LVVQGTAFNWPWPDHFRVVTLPRVDDLEMAIGRIGNFLKSYRQ 403 Lambda K H 0.320 0.138 0.419 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: 612 Number of extensions: 18 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: 429 Length of database: 403 Length adjustment: 31 Effective length of query: 398 Effective length of database: 372 Effective search space: 148056 Effective search space used: 148056 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 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