Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 229 bits (584), Expect = 1e-64 Identities = 139/381 (36%), Positives = 215/381 (56%), Gaps = 24/381 (6%) Query: 5 LNPKAREIEISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPN 64 +N KA E++ G++ V+SL +G+PDF TP HV+ AAK AID+ T YT Sbjct: 18 VNAKALELKAKGVQ-----------VVSLAVGEPDFPTPEHVREAAKTAIDQGFTRYTQV 66 Query: 65 AGYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYP 124 G ELRQAV Y + E+ ++ T G QA+ F+ +L+PGDEV++P P + Sbjct: 67 PGIPELRQAVCGYFARFYGVEAPMEATVV-TNGGKQALYNLFQCLLNPGDEVLVPAPYWV 125 Query: 125 GYEPIINLCGAKPVIVDTTSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEEL 183 Y ++ L G PV V + + GFK+T ++ A+TP T+ ++L PSNPTG S E Sbjct: 126 SYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSRAET 185 Query: 184 KSIAALLKGRNVFVLSDEIYSELTYDRPH-YSIATYLR---DQTIVINGLSKSHSMTGWR 239 +I R++FV+SDEIY L Y+ S+ + + V+NGL+K+ +MTGWR Sbjct: 186 DAIMEWAIARDLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTFAMTGWR 245 Query: 240 IGFLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYD 299 +G+ A D+ K + K+ + S S++QKAAL A+T +D M++ +++R D + Sbjct: 246 VGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRRRDLAHG 305 Query: 300 RLVSM-GLDVVKPSGAFYIFPSIKSFGMTSFDFSMAL----LEDAGVALVPGSSFSTYGE 354 + S G+ KP GAFY+F +++ + S +L +E A VALVPG++F + Sbjct: 306 IVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCTYIMEQANVALVPGAAFG--DD 363 Query: 355 GYVRLSFACSMDTLREGLDRL 375 +R S+A S DTL LD++ Sbjct: 364 ACLRFSYAVSDDTLMIALDKV 384 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: 362 Number of extensions: 18 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: 393 Length of database: 390 Length adjustment: 31 Effective length of query: 362 Effective length of database: 359 Effective search space: 129958 Effective search space used: 129958 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 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