Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_106716014.1 CU100_RS04930 aspartate aminotransferase family protein
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_003010935.1:WP_106716014.1 Length = 401 Score = 470 bits (1210), Expect = e-137 Identities = 234/381 (61%), Positives = 285/381 (74%) Query: 8 TYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSN 67 TYARAD+ FERGEG +L+ G R+LDFAAG+AVN LG+++P+LV AL AQA KLWH SN Sbjct: 12 TYARADLRFERGEGVWLFTDSGIRYLDFAAGIAVNSLGYSHPHLVTALKAQADKLWHLSN 71 Query: 68 LFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQ 127 ++ + GQE L +RL + TFAD VFFTNSGAEA EC K R+YHY G+ R RIITFE Sbjct: 72 IYEIPGQERLGQRLVDNTFADKVFFTNSGAEALECAIKTARRYHYVNGEHERFRIITFEG 131 Query: 128 AFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQGEG 187 AFHGRTLA ++A Q K ++GFGP ++GFD VPFGD+ A++ A+ ETA I +EP+QGEG Sbjct: 132 AFHGRTLATIAAGGQPKYLEGFGPKVEGFDQVPFGDVNALKAAIGPETAAILIEPVQGEG 191 Query: 188 GIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGIGG 247 G+R E LR LR +CDEHGLLL LDE+Q GMGRTGKLFAHEW+GI PD+MAVAKGIGG Sbjct: 192 GVRPVPEEELRALRGLCDEHGLLLILDEVQTGMGRTGKLFAHEWSGIQPDIMAVAKGIGG 251 Query: 248 GFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGLLQ 307 GFPLGACLAT +AA GMTAG HG+TYGGNPLA AVGNAVLD +LE GFL+ VQ + +++ Sbjct: 252 GFPLGACLATAEAAKGMTAGVHGTTYGGNPLAMAVGNAVLDVILEEGFLERVQHVALIMK 311 Query: 308 DRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNVVRLLPPL 367 LA + P VRG+G ++GL C +V ALR LL+V AGDNVVRLLPPL Sbjct: 312 QGLASISDRYPEAISEVRGRGFLIGLKCRVPNTTMVQALRDEHLLTVGAGDNVVRLLPPL 371 Query: 368 NIGEAEVEEAVAILAKTAKEL 388 EA+V EA+A + A+ L Sbjct: 372 VATEADVREALARIEAAAERL 392 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: 496 Number of extensions: 18 Number of successful extensions: 1 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: 401 Length adjustment: 31 Effective length of query: 358 Effective length of database: 370 Effective search space: 132460 Effective search space used: 132460 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 Jul 26 2024. The underlying query database was built on Jul 25 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