Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate WP_106716259.1 CU100_RS09025 cysteine synthase A
Query= BRENDA::A0A0F6AQU1 (342 letters) >NCBI__GCF_003010935.1:WP_106716259.1 Length = 344 Score = 575 bits (1483), Expect = e-169 Identities = 281/341 (82%), Positives = 310/341 (90%) Query: 1 MFNSVLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLR 60 M++SV+DTIGNTPLIRL KAS+LTGC+IYGKAEFLNPGQSVKDRAALYIIRDAE+RGLLR Sbjct: 1 MYDSVIDTIGNTPLIRLKKASDLTGCEIYGKAEFLNPGQSVKDRAALYIIRDAEERGLLR 60 Query: 61 PGGVIVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYR 120 GGVIVEGTAGNTGIGLTMVA+ LGYRT IVIPETQSQEKKDALRLLGAEL+EVPA PY+ Sbjct: 61 RGGVIVEGTAGNTGIGLTMVARTLGYRTVIVIPETQSQEKKDALRLLGAELVEVPAVPYK 120 Query: 121 NPNNYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVA 180 NP+NYV++SGRLAEQ+AKTEPNGAIWANQFDN NRQAH+ETTA EIWRDT+ ++DGFV Sbjct: 121 NPDNYVKISGRLAEQMAKTEPNGAIWANQFDNVANRQAHVETTAPEIWRDTNGKVDGFVC 180 Query: 181 AVGSGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRIT 240 AVGSGGTLAG A GLK R+ NIKI LADP GAAL ++YTTGE K+EG SITEGIGQGR+T Sbjct: 181 AVGSGGTLAGVAQGLKARDANIKIGLADPLGAALFSYYTTGEFKSEGSSITEGIGQGRVT 240 Query: 241 ANLEGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVT 300 ANL GFTPDFSYQIPDAEAL+I+F LV EEGLCLGGSSGINIAGAIR+A+DLGP IVT Sbjct: 241 ANLAGFTPDFSYQIPDAEALEIVFDLVTEEGLCLGGSSGINIAGAIRMARDLGPDKIIVT 300 Query: 301 VLCDYGNRYQSKLFNPAFLRGKSLPVPRWLEKKTEIDIPFE 341 VLCDYGNRYQSK+FNP FLR K+LPVP WLE KT I +PFE Sbjct: 301 VLCDYGNRYQSKMFNPEFLRSKNLPVPAWLEAKTNIPVPFE 341 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: 467 Number of extensions: 10 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: 344 Length adjustment: 29 Effective length of query: 313 Effective length of database: 315 Effective search space: 98595 Effective search space used: 98595 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 Jul 26 2024. The underlying query database was built on Jul 25 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