Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_058931824.1 AU252_RS17580 pyridoxal phosphate-dependent aminotransferase
Query= curated2:P63499 (429 letters) >NCBI__GCF_001484605.1:WP_058931824.1 Length = 406 Score = 551 bits (1419), Expect = e-161 Identities = 273/402 (67%), Positives = 326/402 (81%), Gaps = 2/402 (0%) Query: 28 FAQSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALP 87 F QS KL +VLY+IRGP+ Q A ++EAEGHRILKLNIGNPAPFGFEAPD I+ D+I+ LP Sbjct: 4 FKQSTKLHNVLYDIRGPILQAAQQMEAEGHRILKLNIGNPAPFGFEAPDAILVDMIRHLP 63 Query: 88 YAQGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQV 147 +AQGYSDS+GI SAR AV ++Y G VDD+YLGNGVSELITM+L ALL++GD+V Sbjct: 64 HAQGYSDSRGIFSARTAV-SQYYQTRGIQNIHVDDIYLGNGVSELITMSLMALLNDGDEV 122 Query: 148 LIPSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTG 207 LIP+PDYPLWTAS +LA G PVHYLCDE GWQPD+ DLE+KIT RTK +VVINPNNPTG Sbjct: 123 LIPTPDYPLWTASVALASGKPVHYLCDEESGWQPDLEDLEAKITPRTKGIVVINPNNPTG 182 Query: 208 AVYSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIA-PDMLCLTFNGLSKA 266 AVY E L ++V LA KH L+L ADEIY+KILY+DA HI++A++ D+LCLTF+GLSKA Sbjct: 183 AVYPEETLKKIVALAEKHGLILFADEIYEKILYEDAVHINMAALTGDDVLCLTFSGLSKA 242 Query: 267 YRVAGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVL 326 YRV GYRAGW+AI+GPK+ AS ++EGI LLANMRLC NVPAQHAIQ ALGG+QSI DL+L Sbjct: 243 YRVCGYRAGWMAISGPKKDASDYLEGISLLANMRLCANVPAQHAIQTALGGYQSINDLIL 302 Query: 327 PGGRLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKI 386 PGGRLLEQR+ A+ LN IPGVS + GALY FPRLDPEV+ I DDE+ VLDLL +KI Sbjct: 303 PGGRLLEQRNKAYDMLNAIPGVSTQQARGALYLFPRLDPEVFHIRDDEKFVLDLLKEQKI 362 Query: 387 LVTQGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYR 428 LV+ G FNW PDH R+VTLP +D+ AI R+G+FL Y+ Sbjct: 363 LVSHGRAFNWVRPDHFRMVTLPNVKDIEEAIGRMGDFLSRYQ 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: 555 Number of extensions: 16 Number of successful extensions: 3 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: 406 Length adjustment: 32 Effective length of query: 397 Effective length of database: 374 Effective search space: 148478 Effective search space used: 148478 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 24 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