Align Cystathionine beta-synthase; Beta-thionase; Hemoprotein H-450; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate AZOBR_RS01080 AZOBR_RS01080 cysteine synthase
Query= SwissProt::P32232 (561 letters) >FitnessBrowser__azobra:AZOBR_RS01080 Length = 319 Score = 245 bits (625), Expect = 2e-69 Identities = 140/318 (44%), Positives = 204/318 (64%), Gaps = 18/318 (5%) Query: 72 KILPDILRKIGNTPMVRINRISKNAGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERAG 131 KI IL +G TP+VR+NR++++AG K +++ K EFFN SVKDRI MI+ AERAG Sbjct: 9 KIYDSILDTVGATPLVRVNRLAEDAGAKAQIVGKLEFFNPLASVKDRIGFAMIDAAERAG 68 Query: 132 TLKPG-DTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVRTPT 190 T++PG T++EPTSGNTGI LA AA KGYR I+ MPE MS+E+ +L+ LGAE+V TP Sbjct: 69 TIEPGRTTLVEPTSGNTGIALAFVAAAKGYRLILTMPESMSVERRKMLKLLGAELVLTP- 127 Query: 191 NARFDSPESHVGVAWRLKNEI----PNSHILDQYRNASNPLAHYDDTAEEILQQCDGKVD 246 + E G A R +EI PN+++L Q++NA+NP H + TAEEI + DGK D Sbjct: 128 -----AAEGMKG-AIRRADEIVATDPNAYMLQQFKNAANPEIHRNTTAEEIWKDTDGKAD 181 Query: 247 MLVASAGTGGTITGIARKLKEKCPGCKIIGVDPEGSILAEPEELNQTEQTAYEVEGIGYD 306 L++ GTGGT+TG++ LK + PG + I V+PE S + L+ ++++GIG Sbjct: 182 FLISGVGTGGTLTGVSEVLKARKPGFRTIAVEPEDSPV-----LSGGMPGPHKIQGIGAG 236 Query: 307 FIPTVLDRAVVDRWFKSNDDDSFAFARMLISQEGLLCGGSSGSAMAVAVK-AAQELKEGQ 365 F+P VL++ ++D + ++ +F AR + EG+ G SSG+A+A A++ ++ EG+ Sbjct: 237 FVPDVLNKDLIDEVVRISNQRAFETARKVAKLEGIPVGISSGAALAAALEIGSRPENEGK 296 Query: 366 RCVVILPDSVRNYMSKFL 383 VVILP Y+S L Sbjct: 297 LIVVILPSFAERYLSTAL 314 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: 440 Number of extensions: 26 Number of successful extensions: 7 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: 319 Length adjustment: 32 Effective length of query: 529 Effective length of database: 287 Effective search space: 151823 Effective search space used: 151823 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: 50 (23.9 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