Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF835 HP15_814 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Marino:GFF835 Length = 416 Score = 178 bits (452), Expect = 2e-49 Identities = 116/383 (30%), Positives = 200/383 (52%), Gaps = 7/383 (1%) Query: 6 NPKAREIEISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNA 65 NP + I + GIR+ N+ A +DVI L+IGQPD TP HV A A++ T YT +A Sbjct: 35 NPAMQAIPVPGIRRMVNMAATMKDVIHLSIGQPDLPTPKHVIDAYIDALNAGQTGYTMDA 94 Query: 66 GYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPG 125 G EL A++ Y K+ + ++ I+IT+GA++A+ A +PG + I+ P + Sbjct: 95 GLPELLVALRDYYGKRYNRKLTRDN-ILITSGATEAMYLAISATSAPGRQFIVTDPSFLL 153 Query: 126 YEPIINLCGAKPVIVDT-TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELK 184 Y P+I + G + V T + +L + A+ P T ++L P+NPTG ++ Sbjct: 154 YAPLIRMNGGEVKFVQTRAENNHQLDPDEVIKAMGPRTYALILNNPNNPTGAVYPRSTVE 213 Query: 185 SIAALLKGRNVFVLSDEIYSELTYDRPHYSIATYLR---DQTIVINGLSKSHSMTGWRIG 241 +I R + V +DE+Y L +D ++ D + I+ SK++SM G R+G Sbjct: 214 TILEECAYRGIQVYADEVYDHLIFDDEDFASVLNCSMDLDNIMCISSFSKTYSMAGLRVG 273 Query: 242 FLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL 301 ++ A + K + + H + S A++ SQ A + A+T M + Y++R D V + + Sbjct: 274 WVIASQAAIKSLRRFHMFTTSVANTPSQFAGVAALTGDQQCVRDMVDIYRERRDKVVELV 333 Query: 302 -VSMGLDVVKPSGAFYIFPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLS 360 + + KP GAF+ FP + + D ++ +L++ GV +VPG +F VR+S Sbjct: 334 DQTPYMTGYKPGGAFFAFPDLPPH-VDGSDLALRMLKETGVCMVPGDAFGEGCTNAVRIS 392 Query: 361 FACSMDTLREGLDRLELFVLKKR 383 F+ + + L E DR+ ++ K++ Sbjct: 393 FSTTCEKLEEAFDRVIPWMAKQQ 415 Lambda K H 0.319 0.135 0.388 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: 349 Number of extensions: 18 Number of successful extensions: 6 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: 393 Length of database: 416 Length adjustment: 31 Effective length of query: 362 Effective length of database: 385 Effective search space: 139370 Effective search space used: 139370 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 Aug 03 2021. The underlying query database was built on Aug 03 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