Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate CCNA_01493 CCNA_01493 cysteine synthase
Query= BRENDA::A0A0F6AQU1 (342 letters) >FitnessBrowser__Caulo:CCNA_01493 Length = 332 Score = 484 bits (1247), Expect = e-141 Identities = 236/327 (72%), Positives = 275/327 (84%) Query: 4 SVLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRPGG 63 SVLD IGNTPLIRL++ASE TGC+I GKAEF+NPGQSVKDRAAL IIRDAE +GLLRPGG Sbjct: 6 SVLDAIGNTPLIRLARASEATGCEILGKAEFMNPGQSVKDRAALAIIRDAEAKGLLRPGG 65 Query: 64 VIVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYRNPN 123 IVEGTAGNTGIGL MVA ALGY+T IVIP TQSQEKKDA+RLLGAEL+EV A PY NP+ Sbjct: 66 RIVEGTAGNTGIGLAMVASALGYKTTIVIPRTQSQEKKDAIRLLGAELVEVDAVPYSNPD 125 Query: 124 NYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAAVG 183 NYVR SGRLAE+LA+TEP+G IWANQFDNT NR AH TT EI+ TS ++DGF+ AVG Sbjct: 126 NYVRYSGRLAEELARTEPHGVIWANQFDNTANRDAHYHTTGPEIFDQTSGKVDGFICAVG 185 Query: 184 SGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITANL 243 SGGTLAG A L+ER ++I LADP+GAAL+A+Y GELK+EG SI+EGIGQGRITANL Sbjct: 186 SGGTLAGVAAALRERKPGVRIGLADPYGAALYAWYKDGELKSEGSSISEGIGQGRITANL 245 Query: 244 EGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTVLC 303 EG D +++ D E L++L+ LV+ EGLCLGGS+GIN+AGAI+LA +GPGHTIVTVLC Sbjct: 246 EGLAIDDPFRVSDQEMLEVLYDLVQHEGLCLGGSAGINVAGAIKLATAMGPGHTIVTVLC 305 Query: 304 DYGNRYQSKLFNPAFLRGKSLPVPRWL 330 D+G+RYQSKLFNP FL+ K LP P W+ Sbjct: 306 DHGSRYQSKLFNPVFLKEKGLPTPPWM 332 Lambda K H 0.316 0.137 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: 429 Number of extensions: 13 Number of successful extensions: 1 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: 342 Length of database: 332 Length adjustment: 28 Effective length of query: 314 Effective length of database: 304 Effective search space: 95456 Effective search space used: 95456 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