Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_012102527.1 CKL_RS10715 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q187D4 (421 letters) >NCBI__GCF_000016505.1:WP_012102527.1 Length = 428 Score = 439 bits (1128), Expect = e-127 Identities = 208/422 (49%), Positives = 296/422 (70%), Gaps = 3/422 (0%) Query: 2 YNKETICVQGNYKPGNGEPRVLPLYQSTTFKYSSIDQLAELFDLKVDGHIYSRISNPTIQ 61 Y T CVQ Y+PGNGEPR +P+ QSTTFKY++ + + +LFDL+ G+ YSR+ NPT Sbjct: 4 YKINTKCVQAGYRPGNGEPRQVPIIQSTTFKYNTSEDMGKLFDLEASGYFYSRLQNPTND 63 Query: 62 AFEEKISLLEGGVSSVAVSSGQSANMLAVLNICKSGDSILCSSKVYGGTFNLLGPSLKKF 121 +KI+ +E G +++ SSGQ+AN A+ NIC GD I+ SS +YGGTFNL+ ++ K Sbjct: 64 YVAQKIADMESGTAAMLTSSGQAANFFALFNICNCGDHIVASSSIYGGTFNLISVTMSKM 123 Query: 122 GIDLISFDLDSSEDEIVELAKENTKVVFAETLANPTLEVIDFEKIANVAKRINVPFIVDN 181 GI D +E+E+ + NTK VF ET+ANP L V+D EK A A +VP IVDN Sbjct: 124 GITTTFVSPDCTEEELNAAFQTNTKAVFGETIANPALTVLDIEKFAKAAHAHDVPLIVDN 183 Query: 182 SLASPVLCNPLKYGANIVTHSTTKYLDGHASSVGGIIVDGGNFNW--DNGKFPELVEPDP 239 + +P+ C P ++GA+IVTHSTTKY+DGH ++VGG+IVD GNF+W KFP L PD Sbjct: 184 TFPTPINCRPFEWGADIVTHSTTKYMDGHGAAVGGVIVDSGNFDWMAHADKFPGLCTPDD 243 Query: 240 TYHGISYTQKFG-NAAYATKARVQLLRDYGNCLSPFNAYLTNLNVETLHLRMERHSENAL 298 +YHGI+Y +KFG A+ TK QL+RD+G+ SP +A++ NL +E+LH+RM RH EN Sbjct: 244 SYHGITYAEKFGKEGAFITKCTAQLMRDFGSIQSPQHAFILNLGLESLHVRMPRHCENGQ 303 Query: 299 KIARFLEKHENVDWINYPGLEDNKYYENAKKYLSRGCSGVLSFGVRGGLENAKKFVEKLQ 358 +A FL+ H V ++NY GL +KYY+ A+KYL G GV+SFG++GG E A+ F++ L+ Sbjct: 304 AVAEFLQNHPKVAYVNYCGLPGDKYYKIAQKYLPNGSCGVVSFGLKGGREEAEIFMKNLK 363 Query: 359 IASLVTHVSDVRTCVIHPASTTHRQLTEEQLIASGVLPSLIRLSVGIENVEDLIADLNQA 418 + ++ THV+D R+C ++PA++THRQ+ +E+L +GV LIR+S GIE+ EDLI D++Q+ Sbjct: 364 LVAIETHVADARSCCLNPATSTHRQMNDEELKEAGVPAELIRISCGIEDKEDLIYDISQS 423 Query: 419 LN 420 L+ Sbjct: 424 LD 425 Lambda K H 0.316 0.135 0.387 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: 515 Number of extensions: 14 Number of successful extensions: 3 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: 421 Length of database: 428 Length adjustment: 32 Effective length of query: 389 Effective length of database: 396 Effective search space: 154044 Effective search space used: 154044 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Jul 25 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