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 WP_092056754.1 BQ4888_RS09545 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q55DV9 (387 letters) >NCBI__GCF_900111775.1:WP_092056754.1 Length = 425 Score = 241 bits (616), Expect = 2e-68 Identities = 152/421 (36%), Positives = 225/421 (53%), Gaps = 42/421 (9%) Query: 6 NYKIGTNVIHAGQSADKNTGAVIVPISLSTTFLQPSPGVLHSEYD-------YSRSGNPT 58 ++KI T + G A K T A I I STTF S + +D Y+R GNPT Sbjct: 4 SWKIETQAVQ-GTYAPKATEARIPTICQSTTFKYDSAEHVAKLFDLDLPDPFYTRLGNPT 62 Query: 59 RKAFEECIAACENAKYALSFASG-LATLTTITHLLKSGDEVISIDDVYGGTRRYFTRVAA 117 AFE IA E AL+ +SG AT +I ++ ++G +++ +YGGT F Sbjct: 63 TDAFEGKIALMEGGVGALATSSGQAATALSIMNICRAGQHIVTAGTLYGGTYSLFANTLP 122 Query: 118 NFDLKFSFVDL-STLDDLKNAFTDKTRLVWIETPTNPLLKVADIKAVADYVHSRGATLVV 176 ++ SFV+ S+ +++K F +T+ ++ ET NP L V D + + + G L++ Sbjct: 123 KLGIEVSFVNPDSSAEEIKKHFRPETKALFAETIGNPGLNVLDFEKFSAVARATGVPLLI 182 Query: 177 DNTFMSPYFQNPLDLGADIVMHSVTKYINGHSDCVMGVLA---------------TNNDE 221 DNTF +PY PLD GADIV+HS TKYI+GH+ + GV+ T D Sbjct: 183 DNTFPTPYLCRPLDHGADIVIHSATKYIDGHASSLGGVIVDGGKFDWTSGKFPELTEPDS 242 Query: 222 LYAKLKFLQ----------------NSIGAVPSPFDCFLALRGLKTLHVRMEAHQKNAFA 265 Y L++++ +G PSPF+ FL +GL TL +RME H NA A Sbjct: 243 SYHGLRYVEKFGPSAYIVKARAQYMRDLGVTPSPFNSFLFHQGLTTLPLRMERHSANALA 302 Query: 266 ICNFLEKHPKVERVIYPGLPSHPQHEICKRQM-KGYGGMVVFFVKGSIDQSRSFLENIKL 324 + +FL+ HPKV V YPGL SHP + + +R M KG G++ F +KG+ + F+E ++ Sbjct: 303 LAHFLQGHPKVSWVNYPGLESHPSYPLAQRYMPKGASGVLTFGIKGAREAGIRFMEATRI 362 Query: 325 FALAESLGGVESLIELPSVMTHASVPAEERAKLGISDTLIRLSVGIEDINDLLADISQAL 384 AL +G S + P+ TH + ++ G++ LIRLSVGIE I+DL+AD+ QAL Sbjct: 363 IALVVHVGDARSCVLHPASTTHRQLSEAQQIASGVTPDLIRLSVGIEHIDDLIADVEQAL 422 Query: 385 D 385 + Sbjct: 423 N 423 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: 416 Number of extensions: 20 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: 387 Length of database: 425 Length adjustment: 31 Effective length of query: 356 Effective length of database: 394 Effective search space: 140264 Effective search space used: 140264 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 10 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