Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate 5209443 Shew_1914 aminotransferase AlaT (RefSeq)
Query= curated2:P63499 (429 letters) >FitnessBrowser__PV4:5209443 Length = 404 Score = 506 bits (1304), Expect = e-148 Identities = 242/404 (59%), Positives = 312/404 (77%), Gaps = 1/404 (0%) Query: 26 RAFAQSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQA 85 R +S KL V Y+IRGPVH+ A RLE EGHRILKLNIGNPAPFGFEAP+ I+RD+I Sbjct: 2 RPIIKSNKLDTVCYDIRGPVHKEARRLEDEGHRILKLNIGNPAPFGFEAPEEIVRDVILN 61 Query: 86 LPYAQGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGD 145 LP AQGYS+S+G+ SAR+A+V Y+ + G D++D+Y+GNGVSELI M +Q LL++ D Sbjct: 62 LPSAQGYSESKGLFSARKAIVQHYQSL-GLFGVDIEDIYIGNGVSELIVMAMQGLLNSDD 120 Query: 146 QVLIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNP 205 +VL+PSPDYPLWTA+ L+GG HY CDE W PD+ D++SKI+ RT+ +V+INPNNP Sbjct: 121 EVLVPSPDYPLWTAAVHLSGGKAQHYRCDEESDWFPDLDDIKSKISSRTRGIVLINPNNP 180 Query: 206 TGAVYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSK 265 TGAVYS E+L ++++L R+H ++L ADEIYDKILYD A HI A+++ D+L +TFNGLSK Sbjct: 181 TGAVYSRELLLEIIELCRQHDIILFADEIYDKILYDGAVHIPAATLSDDILTVTFNGLSK 240 Query: 266 AYRVAGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLV 325 +YR AG+R GW+ ++G + A S+IEG+ +LA+MRLC NVP QHAIQ ALGG+QSI +LV Sbjct: 241 SYRAAGFRVGWMMLSGNLKAAKSYIEGLDMLASMRLCSNVPNQHAIQTALGGYQSINELV 300 Query: 326 LPGGRLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEK 385 P GRL QR+ + LN+IPGVSC KP GALYAFP+LD + +++ DDE+LVLDLL +K Sbjct: 301 APEGRLTLQRNTCYELLNQIPGVSCKKPKGALYAFPKLDAKKFNLRDDERLVLDLLKEKK 360 Query: 386 ILVTQGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429 IL+ QGT FNWP PDHLR+V LP DL A+ G+FL SY Q Sbjct: 361 ILLVQGTAFNWPEPDHLRVVFLPHKEDLHKALVEFGDFLTSYSQ 404 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: 554 Number of extensions: 25 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: 404 Length adjustment: 31 Effective length of query: 398 Effective length of database: 373 Effective search space: 148454 Effective search space used: 148454 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