Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_041936994.1 RL_RS34520 hypothetical protein
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000009265.1:WP_041936994.1 Length = 395 Score = 198 bits (504), Expect = 2e-55 Identities = 127/367 (34%), Positives = 202/367 (55%), Gaps = 26/367 (7%) Query: 23 VSAPIYLSTAYRHRGI--------GESTGFDYVRTKNPTRQLVEDAIANLENGARGLAFS 74 VS PI+ ++ + + G + + Y R NPT + E +A LE G AFS Sbjct: 31 VSPPIFQTSLFTYDSYEAMEDVFAGRTRNYIYSRGDNPTVREFELLVARLEGAEDGRAFS 90 Query: 75 SGMAAI-QTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSDEDCLRSKI 133 SG AAI TI++L ++GD ++ LY YRL + G+ + D +D D +R + Sbjct: 91 SGTAAITSTILSLVEAGDRVVAVRHLYNDVYRLLVKLLARLGVAVDFVDPADHDEVRKAL 150 Query: 134 TPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLELGADIVIH 193 + K +++E PT+ + + DI ++ + KE G+ I+DN++ TP+ Q+P++ G DIVIH Sbjct: 151 S-GAKLLYLENPTSFVFELQDIAALSAMAKEAGVTSIIDNSWATPLFQKPIQHGVDIVIH 209 Query: 194 SATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMKTLSLRMRQ 253 +A+KYLGGH+D +AG+VV E + +GA L PF++WLL+RGM+TL +R+++ Sbjct: 210 AASKYLGGHSDTVAGVVVGSKEAIARINATSYPYVGAKLSPFEAWLLLRGMRTLRVRLKE 269 Query: 254 HQANAQELAAFLEEQEEISDVLYP------------GKGGMLSFRLQKEEWVNPFLKALK 301 H+ + LA L+E I V +P G G+ +F L + V F+ +L+ Sbjct: 270 HERSGLLLAGRLKEHSAIGCVRHPAFQEHPGRATLTGYAGLFAFDLNPDIDVARFVNSLR 329 Query: 302 TICFAESLGGVESFITYPATQTHMDIPEEIR--IANGVCNRLLRFSVGIEHAEDLKEDLK 359 I S GG E+ + PA + + IP+ + I GV + +RF+VG+E E L DL+ Sbjct: 330 DIRLGVSWGGPETLVV-PA-KVALQIPDRMTSFIRFGVSEQTVRFAVGLEEPELLWSDLQ 387 Query: 360 QALCQVK 366 QAL K Sbjct: 388 QALHAAK 394 Lambda K H 0.319 0.135 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: 368 Number of extensions: 21 Number of successful extensions: 4 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: 373 Length of database: 395 Length adjustment: 30 Effective length of query: 343 Effective length of database: 365 Effective search space: 125195 Effective search space used: 125195 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 (21.7 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