Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Pf1N1B4_4430 Cystathionine beta-lyase (EC 4.4.1.8)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4430 Length = 919 Score = 189 bits (479), Expect = 4e-52 Identities = 129/382 (33%), Positives = 202/382 (52%), Gaps = 18/382 (4%) Query: 30 RTPEGEHGEALFTT----SSYVFRTAA---DAAARFAGEVPGNVYSRYTNPTVRTFEERI 82 RT +G G A+ S+ +F A DA AR E + Y NPT E+ + Sbjct: 544 RTEKGSGGRAVNVPVTRLSTVLFDNLAQMRDARARRDSERVLS-YGARGNPTAFALEDLV 602 Query: 83 AALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDY 142 LEG + +G++A+ ++ GDHVL++ +V+ L + + FGIQV Y Sbjct: 603 TELEGGYRTRLYGTGLAAVAQTFLAYLRPGDHVLITDAVYAPVRRLARELLEPFGIQVSY 662 Query: 143 PPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPAL 202 D + +A + NTK+ + E P + L EL D+ A+A + +G LLAVDN + + L Sbjct: 663 FA-PDGSGLQAQLQANTKMVYTEVPGSLLYELCDLPAIAALCKPRGILLAVDNTWGSGYL 721 Query: 203 QQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSPFNAWLFL 262 +PL LGAD+ I + TKY+ G + G V R E + + T G +SP +A+L L Sbjct: 722 YRPLTLGADISIMALTKYLCGHSDVVMGSVCTRQEVWQPLSSMSDTFGIAVSPDDAYLVL 781 Query: 263 KGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVSF 322 +G TL R+ H AL +A+WL+ QP ++RV++ LP HP H L RR +G ++SF Sbjct: 782 RGARTLAPRLDVHERQALEIAQWLQAQPQVKRVFHPALPDHPHHALWRRDFNGSNGLLSF 841 Query: 323 DVKGGRDAAW--RFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLI 380 +++ DA + RFIDA ++ + + G ++ + + R S DRA + ++ Sbjct: 842 ELREA-DATYVERFIDALQVFGLGASWGGYESLVT--VADTKDRNSAADRAL----NPVL 894 Query: 381 RVAVGLEDLDDLKADMARGLAA 402 R+ +GLED+D L D+ RG AA Sbjct: 895 RLHIGLEDVDALIEDLQRGFAA 916 Lambda K H 0.319 0.133 0.392 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: 793 Number of extensions: 40 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: 403 Length of database: 919 Length adjustment: 37 Effective length of query: 366 Effective length of database: 882 Effective search space: 322812 Effective search space used: 322812 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: 53 (25.0 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