Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_027490801.1 LRK54_RS04500 acetyl ornithine aminotransferase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_021560695.1:WP_027490801.1 Length = 444 Score = 248 bits (634), Expect = 2e-70 Identities = 156/411 (37%), Positives = 212/411 (51%), Gaps = 40/411 (9%) Query: 15 QVMVPNYA-PAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANK 73 +V+ P+Y F+ G G+ VWD G +DF GIAV GHAHP +V A+ + A K Sbjct: 28 EVISPSYPRDYPFVMSHGRGTEVWDVDGNRFLDFMAGIAVCATGHAHPQVVKAVQDAAAK 87 Query: 74 LWHVSNVFTNEPALRLAHKLVDAT---FAERVFFCNSGAEANEAAFKLARRVAHDRFGTE 130 H+S+ + +E L +L F C SG EA E A KLAR V T Sbjct: 88 FLHISSDYWHEEMTGLGERLAAVAPLGAPAMSFICQSGTEAVEGALKLARYV------TG 141 Query: 131 KYEIVAALNSFHGRTLFTVNVGGQSKYSD--GFGPKITGITHVPY-NDLAAL------KA 181 + + L FHGRT +++ SKY+ GF P + G+THVPY N L A Sbjct: 142 RPRFIGFLGGFHGRTFGSLSFTS-SKYTQQKGFSPTLAGVTHVPYPNPYRPLFAGDDQGA 200 Query: 182 AVSD-------------KTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEV 228 AV D + A+++EP+QGEGG L +L G R LCD H LL+FDEV Sbjct: 201 AVLDYIRMLFQRSVPPSEVAAILIEPMQGEGGYLTPPDGFLAGLRALCDEHGILLIFDEV 260 Query: 229 QTGMGRSGKLFAYQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGN 288 Q+G+GR+G++FA +H+GV PDI+TSAK LG G PI A++ + + G HG TYGGN Sbjct: 261 QSGIGRTGRMFACEHWGVQPDIITSAKGLGSGLPIGAVIAKKSIMSQWKRGAHGNTYGGN 320 Query: 289 PLACAVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVL-- 346 P+ CA A A +D++ + N D F RL ++ Y EVRG GL +G L Sbjct: 321 PVTCAAANATLDLVRGGLMDNAARV-GDHFMARLRELQRDYPCIGEVRGKGLWIGMELIE 379 Query: 347 SDAWKGKAKDIFNA----AEREGLMILQAGPDVIRFAPSLVVEDADIDAGL 393 D K A + A A GL++L G +RF P L V ++D + Sbjct: 380 DDGKKTPATALCEAVVQRAFHNGLLLLSCGTSTVRFMPPLNVSVGEVDEAI 430 Lambda K H 0.320 0.136 0.400 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: 444 Number of extensions: 25 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: 406 Length of database: 444 Length adjustment: 32 Effective length of query: 374 Effective length of database: 412 Effective search space: 154088 Effective search space used: 154088 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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