Align Cystathionine beta-synthase; Beta-thionase; Hemoprotein H-450; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate SMc01174 SMc01174 cysteine synthase A
Query= SwissProt::P32232 (561 letters) >FitnessBrowser__Smeli:SMc01174 Length = 361 Score = 219 bits (558), Expect = 1e-61 Identities = 128/326 (39%), Positives = 188/326 (57%), Gaps = 9/326 (2%) Query: 73 ILPDILRKIGNTPMVRINRISKNAGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERAGT 132 +LP +L IGNTP++R+ +S+ G C +L K EF N G SVKDR +L +I AE++G Sbjct: 18 VLPSVLEAIGNTPLIRLKAVSEATG--CNILGKAEFLNPGQSVKDRAALWIIRQAEKSGQ 75 Query: 133 LKPGDTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVRTPTNA 192 L+PG I+E T+GNTGIGLA+ + GYR +IV+PE S EK D LR LGAE+V P Sbjct: 76 LRPGGVIVEGTAGNTGIGLAVVGSALGYRTVIVIPETQSQEKKDALRLLGAELVEVPA-V 134 Query: 193 RFDSPESHVGVAWRLKNEI----PNSHI-LDQYRNASNPLAHYDDTAEEILQQCDGKVDM 247 + +P ++V ++ RL ++ PN I +Q+ N +N AH D TA EI + DGKVD Sbjct: 135 PYRNPNNYVKISGRLAAQLAETEPNGAIWANQFDNVANRQAHVDTTAPEIWRDTDGKVDG 194 Query: 248 LVASAGTGGTITGIARKLKEKCPGCKIIGVDPEGSILAEPEELNQTEQTAYEV-EGIGYD 306 + + G+GGT+ G+A L+ + KI DPEG+ L + + + + EGIG Sbjct: 195 FICAVGSGGTLAGVAEGLRARNAAIKIGIADPEGAALYNFYAHGELKSSGSSITEGIGQG 254 Query: 307 FIPTVLDRAVVDRWFKSNDDDSFAFARMLISQEGLLCGGSSGSAMAVAVKAAQELKEGQR 366 I L+ D ++ D ++ + LI +EG+ GGS+G +A AV+ A++L G Sbjct: 255 RITANLEDFTPDFAYQIPDAEAVPYVFDLIEKEGICVGGSTGINIAGAVRLARDLGPGHT 314 Query: 367 CVVILPDSVRNYMSKFLSDKWMLQKG 392 V IL D Y SK + ++ KG Sbjct: 315 IVTILCDYGNRYQSKLFNPDFLTSKG 340 Lambda K H 0.317 0.134 0.401 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: 472 Number of extensions: 22 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: 561 Length of database: 361 Length adjustment: 33 Effective length of query: 528 Effective length of database: 328 Effective search space: 173184 Effective search space used: 173184 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: 51 (24.3 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