Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Pf1N1B4_4889 Cystathionine beta-synthase (EC 4.2.1.22)
Query= BRENDA::P37887 (308 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4889 Length = 458 Score = 223 bits (569), Expect = 5e-63 Identities = 125/306 (40%), Positives = 190/306 (62%), Gaps = 14/306 (4%) Query: 7 SITELIGNTPIVKLNRLADENSADVYLKLEYMNPGSSVKDRIGLAMIEAAEKEGKLKAGN 66 ++ ELIGNTP+V+++R D ++LKLE NPG S+KDRIGLAMI+ AE++G+L+ G Sbjct: 8 AVLELIGNTPLVRISRF-DTGPCTLFLKLESQNPGGSIKDRIGLAMIDTAERDGRLRPGG 66 Query: 67 TIIEPTSGNTGIGLAMVAAAKGLKAILVMPDTMSMERRNLLRAYGAELVLTPGAEGMKGA 126 TI+E T+GNTG+GLA+V AKG + +LV+PD MS E+ L+A GAE+ +T G KG Sbjct: 67 TIVEATAGNTGLGLALVGRAKGYRVVLVVPDKMSTEKVLHLKAMGAEVHITRSDVG-KGH 125 Query: 127 IKKAEELAEKHGYFVP-----QQFNNPSNPEIHRQTTGKEIVEQFGDDQLDAFVAGIGTG 181 +++A + +P QFNNP+NP H +T EI Q D +DA V G+G+ Sbjct: 126 PDYYQDVAARLARDIPDAFFADQFNNPANPLAHECSTAPEIWAQTQHD-VDAIVVGVGSA 184 Query: 182 GTITGAGEVLKEAYPSIKIYAVEPSDSPVL----SG--GKPGPHKIQGIGAGFVPDILNT 235 GT+TG + P++++ +P S + SG G PG ++GIG F+P I + Sbjct: 185 GTLTGLTRFFQRVQPNLEMVLADPVGSVMAEYSRSGTLGTPGSWAVEGIGEDFIPSIADL 244 Query: 236 EVYDEIFPVKNEEAFEYARRAAREEGILGGISSGAAIYAALQVAKKLGKGKKVLAIIPSN 295 + + + +EE+F++AR+ R EGILGG S+G + AAL+ ++ + K+V++ + Sbjct: 245 SSVRKAYSISDEESFDHARQLLRAEGILGGSSTGTLLAAALRYCREQTEPKRVVSFVCDT 304 Query: 296 GERYLS 301 G RYLS Sbjct: 305 GTRYLS 310 Lambda K H 0.313 0.134 0.373 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: 294 Number of extensions: 14 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: 308 Length of database: 458 Length adjustment: 30 Effective length of query: 278 Effective length of database: 428 Effective search space: 118984 Effective search space used: 118984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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