Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate CA265_RS13740 CA265_RS13740 cysteine synthase
Query= BRENDA::E5LPF4 (309 letters) >FitnessBrowser__Pedo557:CA265_RS13740 Length = 348 Score = 248 bits (632), Expect = 2e-70 Identities = 137/308 (44%), Positives = 196/308 (63%), Gaps = 5/308 (1%) Query: 6 DNITGLIGNTPLLKLNRVVPEDAADVYVKLEFFNPGGSVKDRIALAMIEDAEYKGVLKPG 65 ++++ L+GNTP+L+L +YVK E +N GS+KDR+AL ++ A +G +K G Sbjct: 18 EHLSLLVGNTPMLELTYTYQGSLGKIYVKCEHYNLTGSIKDRMALYTLKKAYAEGKIKAG 77 Query: 66 GTIVEPTSGNTGIGLALVAAAKGYHLIITMPETMSVERRALMRGYGAELILTPGAD-GMP 124 IVE TSGNTGI A + A G+ + I MP +S ER +++ GAE+IL + G Sbjct: 78 DRIVEATSGNTGIAFAAIGKALGHPVTIIMPNWLSKERMDIIKSLGAEIILVSKEEGGFI 137 Query: 125 GAIKKAQAL-SKENGYFLPMQFQNPANPDVHERTTGQEIIRS--FDGGTPDAFVAGVGTG 181 G+IK A+ + + + FLP QF+N ANP+ HE TTG+EI +PDAFVAGVGTG Sbjct: 138 GSIKLAEKMAASDPNIFLPKQFENIANPEAHEHTTGKEIWEQLRLKNLSPDAFVAGVGTG 197 Query: 182 GTLTGVGRALRKINPQVQIYALEAAESPMLKEGHG-GKHKIQGISAGFIPDVLDTNLYQD 240 GT+ GVG LRK N ++I+ LE AESP L G+ G H+IQGIS FIP+++ N + Sbjct: 198 GTIMGVGNFLRKQNADIKIHPLEPAESPTLTTGYKVGSHRIQGISDEFIPEIVKLNELDE 257 Query: 241 IIEVTSDQAIDMARHVSHEEGFLPGISAGANIFGAIEIAKKLGKGKSVVTVAPDNGERYL 300 +++V AI MA+ ++ + G GIS+GAN+ GAI+ +K+G VVT+ D+ ++YL Sbjct: 258 VLQVNDGDAILMAQKLAEKLGLAVGISSGANVIGAIKQQQKMGADSCVVTIFSDSNKKYL 317 Query: 301 STDLFKFE 308 STDL K E Sbjct: 318 STDLMKVE 325 Lambda K H 0.316 0.137 0.390 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: 287 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: 309 Length of database: 348 Length adjustment: 28 Effective length of query: 281 Effective length of database: 320 Effective search space: 89920 Effective search space used: 89920 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: 49 (23.5 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