Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_012853702.1 TCUR_RS16645 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000024385.1:WP_012853702.1 Length = 431 Score = 168 bits (425), Expect = 3e-46 Identities = 139/417 (33%), Positives = 192/417 (46%), Gaps = 44/417 (10%) Query: 1 VIPVVMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQ-A 59 V+P M Y I G+G + +G +LDF AG+ N+LG+ + +A+ Q A Sbjct: 11 VMPNWMALYYERPIEIVSGKGVRVTDAEGNTYLDFFAGIITNILGYDVEEVRQAVERQLA 70 Query: 60 HKLWHTSNLFRVAGQESLAKRLTEATFADT--VFFTNSGAEAWECGAKLIRKYHYEKGDK 117 + HTS + + GQ LA+++ + VFF NSG EA E A L+ Y + Sbjct: 71 TGVVHTSTAYLLRGQVELAEKIVALSGIKDAKVFFVNSGTEANET-ALLLATYA-----R 124 Query: 118 ARTRIITFEQAFHGRTLAAVSA-AQQEKLIKGFGPL----LDGFD--LVPFGDL------ 164 +++ Q++HGR+ A+ A + + PL L G D L F L Sbjct: 125 KSNQVLAMRQSYHGRSFGAIGVTANRSWKNNAYTPLTVHFLHGGDRHLPQFAHLSDADFI 184 Query: 165 ----EAVRNAVTDETAG----ICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEI 216 E +R+ + T G + EPIQG GG +E+ DE+G L DE+ Sbjct: 185 KVCTEDLRHVLATATGGDVAALIAEPIQGVGGFTMPPDGLYAAYKEVLDEYGALFISDEV 244 Query: 217 QCGMGRTGK-LFAHEWAGITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGG 275 Q G GRTG+ F G+TPD+M AKG+G GF +G +A A T ST+GG Sbjct: 245 QTGWGRTGQSFFGIHNHGVTPDIMTFAKGLGNGFAVGGVVARGDLMDAPHA-TGLSTFGG 303 Query: 276 NPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLML---- 331 NP+A A NA LD +L+ + R G LL D L P V VRGKGLM Sbjct: 304 NPIAMAAANATLDYILDHDLQSNAARQGALLLDGLKEAAPRLPVV-GAVRGKGLMFAVEL 362 Query: 332 -----GLACGPAVGDVVVALRANGLLSVPAG--DNVVRLLPPLNIGEAEVEEAVAIL 381 G P V+ R GLL G NV+R+ PPL I E + E + IL Sbjct: 363 VEPGTGEPSPPLAAAVMEETRKRGLLVGKGGLYGNVIRMAPPLTITEEDAREGLGIL 419 Lambda K H 0.321 0.139 0.414 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: 451 Number of extensions: 36 Number of successful extensions: 7 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: 389 Length of database: 431 Length adjustment: 31 Effective length of query: 358 Effective length of database: 400 Effective search space: 143200 Effective search space used: 143200 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 10 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