Align Cystathionine beta-synthase; Beta-thionase; Hemoprotein H-450; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate 3607478 Dshi_0891 cysteine synthase A (RefSeq)
Query= SwissProt::P32232 (561 letters) >FitnessBrowser__Dino:3607478 Length = 360 Score = 202 bits (515), Expect = 1e-56 Identities = 130/330 (39%), Positives = 185/330 (56%), Gaps = 25/330 (7%) Query: 68 TKSPKILPDILRKIGNTPMVRINRISKNAGLKCELLAKCEFFNAGGSVKDRISLRMIEDA 127 T + K +L +GNTP++RIN ++ EL K EFFN SVKDR++L +IE A Sbjct: 11 TGNGKTYDSVLDTVGNTPVIRINNLAPEG---VELYVKAEFFNPAASVKDRLALNIIEAA 67 Query: 128 ERAGTLKPGDTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVR 187 ERAGTLKPG T++E TSGNTGIGLA+ A KGY +I M E S+E+ ++R LGA++V Sbjct: 68 ERAGTLKPGQTVVEATSGNTGIGLAMVCAQKGYPLVITMAESFSIERRKLMRLLGAKVVL 127 Query: 188 TPTNAR-FDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDDTAEEILQQCDG-KV 245 TP + F V +A E + Q+ A+N H + TA+EIL +G K+ Sbjct: 128 TPRAEKGFGMYRKAVELA-----EANGWFLASQFETAANAEMHENTTAQEILGDFEGCKL 182 Query: 246 DMLVASAGTGGTITGIARKLKEKCPGCKIIGVDPE-----GSILAEPEELN---QTEQTA 297 D +V GTGGT+TG+ R L++ P KII +P GS +A+ + N +A Sbjct: 183 DYIVTGYGTGGTVTGLGRVLRKARPETKIILTEPANAQLLGSGIAQDRDPNGAPAVSHSA 242 Query: 298 YE---VEGIGYDFIPTVL----DRAVVDRWFKSNDDDSFAFARMLISQEGLLCGGSSGSA 350 +E ++G DFIP VL D+ D D A+AR L ++EG+L G S GS Sbjct: 243 FEPHPIQGWTPDFIPKVLQESIDQGFYDALLPVAGADGIAWARRLAAEEGILTGISGGST 302 Query: 351 MAVAVKAAQELKEGQRCVVILPDSVRNYMS 380 A++ + A+ EG + +LPD+ Y+S Sbjct: 303 FAISHEVAKTAPEGSVILCMLPDTGERYLS 332 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: 477 Number of extensions: 23 Number of successful extensions: 5 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: 360 Length adjustment: 33 Effective length of query: 528 Effective length of database: 327 Effective search space: 172656 Effective search space used: 172656 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