Align cysteine synthase (EC 2.5.1.47); cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate Synpcc7942_B2664 Synpcc7942_B2664 cysteine synthase
Query= BRENDA::F9UT54 (303 letters) >FitnessBrowser__SynE:Synpcc7942_B2664 Length = 329 Score = 202 bits (513), Expect = 1e-56 Identities = 126/308 (40%), Positives = 177/308 (57%), Gaps = 17/308 (5%) Query: 8 ELIGHTPLMALPIEVPNH-SHIYAKLEMFNPGGSIKDRLGAYLIEDGLQRGRVNAKTTII 66 + IG TPL+ L V + + AK+E NP S+K R+GA +I D QRG + +I Sbjct: 13 QTIGKTPLVRLNRIVKGAPATVLAKIEGRNPAYSVKCRIGAAMIWDAEQRGLLGPGKELI 72 Query: 67 EPTAGNTGIGLALATQAHHLRTILVVPEKFSMEKQVLMQALGAEIVHTPSEEGIKGAIRK 126 EPT+GNTGI LA A + L +PE S+E++ L+ A GA++V T +G+ GA+R+ Sbjct: 73 EPTSGNTGIALAFVAAARGIPLTLTMPETMSLERRKLLAAYGAKLVLTEGVKGMTGAVRR 132 Query: 127 AEALAATISNSYVPM-QFKNPANPAAYYHTLAPEILADMPAPITAFVAGAGSGGTFAGVA 185 AE +AA+ + YV + QF+NPANPA + T PEI D I V+G G+GGT GV+ Sbjct: 133 AEDIAASDPDRYVLLQQFRNPANPAIHEQTTGPEIWEDTGGAIDILVSGVGTGGTITGVS 192 Query: 186 AYL-QAQDSATKAVVVEPE----------GSILNGGPAHAHRTEGIGVEFIPPFFDQVRI 234 Y+ Q Q +V VEPE G L GP H+ +GIG FIP D + Sbjct: 193 RYIKQTQGKPILSVAVEPEASPVISQQRSGLPLKPGP---HKIQGIGAGFIPENLDLSLV 249 Query: 235 DQTLTIADNDAFAQVRHLARDHGLLIGSSSGAALAASLQLATNLP-ANSHIVTIFPDSSE 293 DQ +++ +A A R LA++ GL+ G S GAA+AA+++LA A IV + PDS E Sbjct: 250 DQVERVSNEEAIAYARRLAQEEGLISGISCGAAVAAAVRLAQQSEHAGKTIVVVLPDSGE 309 Query: 294 RYLSQKIY 301 RYLS ++ Sbjct: 310 RYLSTALF 317 Lambda K H 0.317 0.133 0.378 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: 271 Number of extensions: 16 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: 303 Length of database: 329 Length adjustment: 27 Effective length of query: 276 Effective length of database: 302 Effective search space: 83352 Effective search space used: 83352 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 (21.7 bits) S2: 48 (23.1 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