Align homocysteine synthase Met17; EC 2.5.1.49 (characterized)
to candidate WP_012970751.1 ALVIN_RS07635 aminotransferase class V-fold PLP-dependent enzyme
Query= CharProtDB::CH_124469 (429 letters) >NCBI__GCF_000025485.1:WP_012970751.1 Length = 425 Score = 457 bits (1175), Expect = e-133 Identities = 232/422 (54%), Positives = 297/422 (70%), Gaps = 2/422 (0%) Query: 9 ETLQLHAGQEPDAATSSRAVPIYATTSYVFRDCDHGGRLFGLQEPGYIYSRMMNPTADVF 68 ETL +HAG EPD AT S A PIY TTSY F D HG LF L+ G IY+R+MNPT+DV Sbjct: 4 ETLAIHAGFEPDPATKSVATPIYQTTSYAFDDTQHGADLFDLKVAGNIYTRIMNPTSDVL 63 Query: 69 EKRIAALEHGAAAIATSSGTSALFMALTTLAKAGDNIVSTSYLYGGTYNLFKVTLPRLGI 128 EKR++ALE G A+A +SG +A+ ++ TLA+AGDNI++ S LYGG+YNLF TLPRLGI Sbjct: 64 EKRVSALEGGVGALALASGMAAVTNSILTLAQAGDNIIAVSTLYGGSYNLFAHTLPRLGI 123 Query: 129 TTKFVNGDDPNDLAAQIDENTKAVYVESIGNPMYNVPDFERIAEVAHAAGVPLMVDNTFG 188 +F +D +AAQID TKAV+ ESIGNP NV D +A++AHA GVPL+VDNT Sbjct: 124 QVRFAAPNDIEGMAAQIDARTKAVFCESIGNPAGNVADIAPMADMAHAHGVPLIVDNTV- 182 Query: 189 GGGYLVRPIDHGADIVTHSATKWIGGHGTTIGGVIVDSGKFDWKKNSKRFPEFNEPHPGY 248 YL RP +HGADIV H+ TK++GGHGTTIGG +VDSG+F W ++++RF NEP Y Sbjct: 183 PTPYLCRPFEHGADIVVHALTKYMGGHGTTIGGALVDSGRFPWAEHAERFSLLNEPDISY 242 Query: 249 HGMVFTETFGNLAYAFACRTQTLRDVGGNANPFGVFLLLQGLETLSLRMERHVQNAFALA 308 HG+V+TET G AY R LR++G +PF FL+LQG+ETL +RM+RH +NA A+A Sbjct: 243 HGVVYTETMGEAAYIARARVVPLRNMGAAISPFNSFLILQGIETLPVRMDRHCENAIAVA 302 Query: 309 KYLEKHPKVNWVSYPGLESHVSHKLAKKYLKNG-YGAVLSFGAKGGPDQSRKVVNALKLA 367 YL+ HPKV WV Y GL + L ++Y+ ++LSFG KGG + + ++ALKL Sbjct: 303 NYLQDHPKVAWVRYAGLPDSPDYPLVQRYMDGARASSILSFGIKGGRETGGRFIDALKLT 362 Query: 368 SQLANVGDAKTLVIAPAYTTHLQLTDEEQISAGVTKDLIRVAVGIEHIDDIIADFAQALE 427 +L N+GDAKTL PA TTH QL+ EE AGV++DLIR+++GIEHIDDII D QAL Sbjct: 363 VRLVNIGDAKTLACHPATTTHRQLSPEELKRAGVSEDLIRLSIGIEHIDDIIEDLDQALA 422 Query: 428 VA 429 A Sbjct: 423 AA 424 Lambda K H 0.318 0.135 0.399 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: 571 Number of extensions: 25 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: 429 Length of database: 425 Length adjustment: 32 Effective length of query: 397 Effective length of database: 393 Effective search space: 156021 Effective search space used: 156021 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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