Align Cystathionine gamma-lyase; CGL; CSE; Cysteine desulfhydrase; Cysteine-protein sulfhydrase; Gamma-cystathionase; Homocysteine desulfhydrase; EC 4.4.1.1; EC 4.4.1.2 (characterized)
to candidate CA265_RS08190 CA265_RS08190 cystathionine gamma-synthase
Query= SwissProt::Q55DV9 (387 letters) >FitnessBrowser__Pedo557:CA265_RS08190 Length = 371 Score = 314 bits (804), Expect = 3e-90 Identities = 169/375 (45%), Positives = 231/375 (61%), Gaps = 10/375 (2%) Query: 11 TNVIHAGQSADKNTGAVIVPISLSTTFLQPSPGVLHSEYDYSRSGNPTRKAFEECIAACE 70 T IHA TG V P++LSTTF + + G + YSR NP R A E +A E Sbjct: 5 TLAIHASNLVKSITGDVTPPLNLSTTFFRDAEGGYPGGHMYSRVSNPNRSALENTVAKLE 64 Query: 71 NAKYALSFASGLATLTTITHLLKSGDEVISIDDVYGGTRRYFTRVAANFDLKFSFVDLST 130 + A +F+SG + LK G +I+ DD+Y G ++ + N L+F F+D + Sbjct: 65 YGEDAAAFSSGNTCGLVLFQALKPGSHIIAPDDMYWGIKKQLLTIF-NDSLEFDFIDQTD 123 Query: 131 LDDLKNAFTDKTRLVWIETPTNPLLKVADIKAVADYVHSRGATLVVDNTFMSPYFQNPLD 190 LD ++ + T+L+WIETP+NPLLKV DI+ +A ++ TL D+TF SP QNP+ Sbjct: 124 LDLIQASIRSNTKLIWIETPSNPLLKVTDIEEIAKIAKAKNITLACDSTFASPILQNPIL 183 Query: 191 LGADIVMHSVTKYINGHSDCVMGVLAT-NNDELYAKLKFLQNSIGAVPSPFDCFLALRGL 249 LGADIVMHS TKY+ GHSD + G+L T DEL+ K+K +Q + GAVPSPFDCFL R + Sbjct: 184 LGADIVMHSSTKYLGGHSDVLGGILVTAKKDELWEKIKNIQQTGGAVPSPFDCFLLTRSI 243 Query: 250 KTLHVRMEAHQKNAFAICNFLEKHPKVERVIYPGLPSHPQHEICKRQMKGYGGMVVFFVK 309 KTL RM+ H +N I ++L HP VE V YPGL SHPQH+I K+QMK +GGM+ F VK Sbjct: 244 KTLAYRMKGHCENGKIIADYLNAHPNVEAVFYPGLESHPQHDIAKKQMKDFGGMMSFLVK 303 Query: 310 GSIDQSRSFLENIKLFALAESLGGVESLIELPSVMTHASVPAEERAKLGISDTLIRLSVG 369 G ++ + + ++LFA A SLGGVESLIE SV + L+R+SVG Sbjct: 304 GDVEAAHKVVNKVQLFAQATSLGGVESLIE-----HRYSVEGPDSK---TPKNLLRISVG 355 Query: 370 IEDINDLLADISQAL 384 +E +D++AD++QAL Sbjct: 356 LEHADDIIADLAQAL 370 Lambda K H 0.320 0.135 0.394 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: 393 Number of extensions: 15 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: 387 Length of database: 371 Length adjustment: 30 Effective length of query: 357 Effective length of database: 341 Effective search space: 121737 Effective search space used: 121737 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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