Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_013450565.1 CALNI_RS02185 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::acidovorax_3H11:Ac3H11_2452 (415 letters) >NCBI__GCF_000183405.1:WP_013450565.1 Length = 426 Score = 208 bits (530), Expect = 2e-58 Identities = 138/409 (33%), Positives = 204/409 (49%), Gaps = 23/409 (5%) Query: 25 GAIHQPIHTSVQYGYDKVEDLIAVFQGTAKGGFNYARQGTPTTAALEAKITKMERGHGTI 84 GA PI+ + Y + + +F G Y R PT LE ++ + +G I Sbjct: 19 GARAVPIYQTTSYVFKSTDHAANLFALKEFGNI-YTRLMNPTQDVLEKRLAALHKGTSAI 77 Query: 85 VFSSGMAGICAVFLTLLKAGDHLVASQFVFGNTNSVLG-TLADLGVEVTTVDVTDAANVA 143 SSG I L + GD++V++ F++G T ++ T+ L EV VD + N A Sbjct: 78 AVSSGQTAITYSILNITSPGDNIVSTSFLYGGTYNLFKYTMKKLCREVRFVDSSKPENFA 137 Query: 144 AALRPNTRMVFVETIANPGTQIPDLEGIGALCKAHGALYVVDNTVASPYLFRAATVGAGL 203 A+ NT+ +++E+I NP + D + I + HG +VDNTV SPY+ GA + Sbjct: 138 NAIDENTKAIYIESIGNPKNNVNDYKAIADIAHKHGIPLIVDNTV-SPYILNPFEYGADI 196 Query: 204 VVNSLTKSIGGLGDALGGAITDTGLYDWSR-----------------YPNIFAAYRKGDA 246 VV SLTK G G +LGGAI + G + W+ Y + F + K A Sbjct: 197 VVYSLTKFATGNGTSLGGAIVEKGDFPWNNGKFNEMTEPDDSYHGLVYWDAFGWHDKAAA 256 Query: 247 KGWGL-QQLRKKGLRDMGGTLSSHAAHQLALGAETLALRMDRTSATALALAQWLEAHPAI 305 +G Q++R + LRDMG +S A + G ETL LRM + AL +A++LE HP + Sbjct: 257 RGCIFTQKIRLQLLRDMGACISPFNAFMIIEGLETLPLRMKKHCDNALKVAEFLEKHPNV 316 Query: 306 ARVHYPLLPSHPQHAFAKKHLKAG-SWLLSFELRDPDQC-LPVCNRLQLPIKATGLADTR 363 V+YP LPSHP H AKK+LK ++ F ++ + N L++ + D R Sbjct: 317 GWVNYPGLPSHPDHENAKKYLKGNYGAIIGFGVKGGYEAGKRFINSLKMISHLANIGDAR 376 Query: 364 TLIIPVAHTIFWEAGPAVRASMGIADSMIRLSVGLEEVEDLLADFEQAL 412 +L+I A T + P R G+ D IRLSVG+E VED++ D AL Sbjct: 377 SLVIHPASTTHQQLSPEDRIKSGVTDDFIRLSVGIENVEDIIEDLNNAL 425 Lambda K H 0.320 0.134 0.398 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: 389 Number of extensions: 15 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: 415 Length of database: 426 Length adjustment: 32 Effective length of query: 383 Effective length of database: 394 Effective search space: 150902 Effective search space used: 150902 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 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