Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate 201879 SO2741 adenosylmethionine--8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >FitnessBrowser__MR1:201879 Length = 461 Score = 152 bits (383), Expect = 2e-41 Identities = 132/402 (32%), Positives = 197/402 (49%), Gaps = 43/402 (10%) Query: 20 EGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNLFRVAGQE---S 76 +G L DGR+ +D + V G+ +P ++ A+ Q H+L H +F E Sbjct: 34 QGCELELVDGRKLIDGTSSWWACVHGYGHPAILTAMEQQLHQLSHV--MFGGITHEPAIE 91 Query: 77 LAKRLTEATFADT--VFFTNSGAEAWECGAKLIRKYHYEK----GDKA-RTRIITFEQAF 129 L K+L T VF +SG+ A E K+ +Y + KA + RI+T ++ + Sbjct: 92 LCKKLLAMTCEPLTKVFLCDSGSIAVEVAIKMALQYWQGQDLPLAQKAQKQRILTVKKGY 151 Query: 130 HGRTLAAVSAAQQE---------KLIKG---------FGPLLDGFDLVPFGDLEAVRNAV 171 HG T AA+S E +IK FG L DL P ++ + Sbjct: 152 HGDTFAAMSVCDPEGGMHTMFGEAVIKQCFVDAPQTPFGESLHQDDLAP---MQRILREQ 208 Query: 172 TDETAGICLEPI-QGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHE 230 + A + +EPI QG GG+R S E+LRGLR +CDE+ +LL LDEI G GRTGKLFA+E Sbjct: 209 HQDIAAVIIEPIMQGAGGMRFYSSEYLRGLRALCDEYNVLLILDEIATGFGRTGKLFAYE 268 Query: 231 WAGITPDVMAVAKGIGGGF-PLGACLATEKAASGMT---AGT--HGSTYGGNPLATAVGN 284 ITPD++ + K + GG+ L A L T+ A G++ AG HG T+ GNPLA A Sbjct: 269 HTDITPDILCLGKALTGGYISLAATLCTDNVAQGISQSPAGVFMHGPTFMGNPLACAAAC 328 Query: 285 AVLDKVLEPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVV 344 A LD + + + V I +Q LA + + P+V K VR G + L AV + Sbjct: 329 ASLDLINQQEWPAQVAAIEQQMQRELADAI-DIPSV-KAVRVLGAVGVLEMHQAVNTAAL 386 Query: 345 ALRANGL-LSVPAGDNVVRLLPPLNIGEAEVEEAVAILAKTA 385 + L + V N++ ++PP I A++ + + + A Sbjct: 387 QQQFVDLGVWVRPFANLIYIMPPYVISSAQLSQLTQAMKQVA 428 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: 421 Number of extensions: 21 Number of successful extensions: 4 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: 461 Length adjustment: 32 Effective length of query: 357 Effective length of database: 429 Effective search space: 153153 Effective search space used: 153153 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 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