Align homocysteine synthase Met17; EC 2.5.1.49 (characterized)
to candidate Ac3H11_2452 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= CharProtDB::CH_124469 (429 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2452 Length = 415 Score = 229 bits (584), Expect = 1e-64 Identities = 146/424 (34%), Positives = 221/424 (52%), Gaps = 17/424 (4%) Query: 4 ESEHFETLQLHAGQEPDAATSSRAVPIYATTSYVFRDCDHGGRLF-GLQEPGYIYSRMMN 62 +++ F T +HA + A + PI+ + Y + + +F G + G+ Y+R Sbjct: 5 QNQSFTTQIVHADRLGGAEQGAIHQPIHTSVQYGYDKVEDLIAVFQGTAKGGFNYARQGT 64 Query: 63 PTADVFEKRIAALEHGAAAIATSSGTSALFMALTTLAKAGDNIVSTSYLYGGTYNLFKVT 122 PT E +I +E G I SSG + + TL KAGD++V++ +++G T ++ T Sbjct: 65 PTTAALEAKITKMERGHGTIVFSSGMAGICAVFLTLLKAGDHLVASQFVFGNTNSVLG-T 123 Query: 123 LPRLGITTKFVNGDDPNDLAAQIDENTKAVYVESIGNPMYNVPDFERIAEVAHAAGVPLM 182 L LG+ V+ D ++AA + NT+ V+VE+I NP +PD E I + A G + Sbjct: 124 LADLGVEVTTVDVTDAANVAAALRPNTRMVFVETIANPGTQIPDLEGIGALCKAHGALYV 183 Query: 183 VDNTFGGGGYLVRPIDHGADIVTHSATKWIGGHGTTIGGVIVDSGKFDWKKNSKRFPEFN 242 VDNT YL R GA +V +S TK IGG G +GG I D+G +DW + F + Sbjct: 184 VDNTVASP-YLFRAATVGAGLVVNSLTKSIGGLGDALGGAITDTGLYDWSRYPNIFAAYR 242 Query: 243 EPHPGYHGMVFTETFGNLAYAFACRTQTLRDVGGNANPFGVFLLLQGLETLSLRMERHVQ 302 + G+ R + LRD+GG + L G ETL+LRM+R Sbjct: 243 KGDAKGWGLQ------------QLRKKGLRDMGGTLSSHAAHQLALGAETLALRMDRTSA 290 Query: 303 NAFALAKYLEKHPKVNWVSYPGLESHVSHKLAKKYLKNGYGAVLSFGAKGGPDQSRKVVN 362 A ALA++LE HP + V YP L SH H AKK+LK G +LSF + PDQ V N Sbjct: 291 TALALAQWLEAHPAIARVHYPLLPSHPQHAFAKKHLKAG-SWLLSFELR-DPDQCLPVCN 348 Query: 363 ALKLASQLANVGDAKTLVIAPAYTTHLQLTDEEQISAGVTKDLIRVAVGIEHIDDIIADF 422 L+L + + D +TL+I A+T + + S G+ +IR++VG+E ++D++ADF Sbjct: 349 RLQLPIKATGLADTRTLIIPVAHTIFWEAGPAVRASMGIADSMIRLSVGLEEVEDLLADF 408 Query: 423 AQAL 426 QAL Sbjct: 409 EQAL 412 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: 404 Number of extensions: 23 Number of successful extensions: 5 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: 415 Length adjustment: 32 Effective length of query: 397 Effective length of database: 383 Effective search space: 152051 Effective search space used: 152051 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: 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