Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate Pf1N1B4_4889 Cystathionine beta-synthase (EC 4.2.1.22)
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4889 Length = 458 Score = 270 bits (689), Expect = 1e-76 Identities = 175/458 (38%), Positives = 248/458 (54%), Gaps = 20/458 (4%) Query: 7 ISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGT 66 + ELIG TPLVR+ S G T+ K+E NPGGS KDRI + MI+ AE G+L+PGGT Sbjct: 9 VLELIGNTPLVRI-SRFDTGPCTLFLKLESQNPGGSIKDRIGLAMIDTAERDGRLRPGGT 67 Query: 67 IVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPA 126 IVE T+GNTG+GLALV + +GY+ V V PDK+S +K L A GAEV + + V P Sbjct: 68 IVEATAGNTGLGLALVGRAKGYRVVLVVPDKMSTEKVLHLKAMGAEVHITRSDVGKGHPD 127 Query: 127 SYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTI 186 Y V+ RL RDI A+ DQ+ NP P +H +T PEIWA T+ V V G+G+ GT+ Sbjct: 128 YYQDVAARLARDIPDAFFADQFNNPANPLAHECSTAPEIWAQTQHDVDAIVVGVGSAGTL 187 Query: 187 TGAGRYLKEVSGGRVRIVGADPEGSVY-----SGGAGRP--YLVEGVGEDFWPAAYDPSV 239 TG R+ + V + +V ADP GSV SG G P + VEG+GEDF P+ D S Sbjct: 188 TGLTRFFQRVQ-PNLEMVLADPVGSVMAEYSRSGTLGTPGSWAVEGIGEDFIPSIADLSS 246 Query: 240 PDEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGR 299 + ++SD +SFD R+L R E +L G S G + AAL+ E +V + D G Sbjct: 247 VRKAYSISDEESFDHARQLLRAEGILGGSSTGTLLAAALRYCREQTEPKRVVSFVCDTGT 306 Query: 300 GYMSKIFNDAWMSSYGFLRSRLDGSTEQSTVGDVLRRKSGALPALVHTHPSETVRDAIGI 359 Y+SK++ND WM+ G L + G + D++ R+ +V P +T+ A Sbjct: 307 RYLSKVYNDQWMNDQGLLARKRYGD-----LRDLIARRFED-GRVVSVGPDDTLLTAFQR 360 Query: 360 LREYGVSQMPVVGAEPPVMAGEVAGSVSERELLSAVFEGRAKLADAVSAHMSPPLRMIGA 419 +R VSQ+PV+ V + G + E ++L V E V++ M+ L + Sbjct: 361 MRLADVSQLPVL-----VDGQRLVGVIDESDILFGVHEDATHFRMTVTSAMTDKLETLPP 415 Query: 420 GELVSAAGKALRDWDALMVVEEGKPVGVITRYDLLGFL 457 G ++ L ++ + G+ITR D+L L Sbjct: 416 GASLAELEAVLDRGLVAIIADTSGFHGLITRVDMLNHL 453 Lambda K H 0.316 0.135 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: 599 Number of extensions: 35 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: 464 Length of database: 458 Length adjustment: 33 Effective length of query: 431 Effective length of database: 425 Effective search space: 183175 Effective search space used: 183175 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 (21.6 bits) S2: 51 (24.3 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