Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate Ac3H11_34 Methionine gamma-lyase (EC 4.4.1.11)
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_34 Length = 434 Score = 306 bits (784), Expect = 7e-88 Identities = 175/394 (44%), Positives = 235/394 (59%), Gaps = 12/394 (3%) Query: 6 TGHQGISGPATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVG-------GLRGGFEYAR 58 T +G +TRAIH GY P GA+ PI+ S+T+A V G G+ Y R Sbjct: 5 TDRSPATGFSTRAIHHGYNPADHQGALVPPIHTSATYAFPDVAYGARCFAGQEPGYFYTR 64 Query: 59 TGNPTRAALEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLI 118 NPT A LE LAA+EEGA A F SGM A L +ML PGD ++ YG TF + Sbjct: 65 IANPTLALLEGRLAALEEGAGAVVFGSGMGAITATLWSMLEPGDEILADLTLYGCTFSFL 124 Query: 119 DKVFTRWDVQYTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSA 178 R+ V V + D V A+T +TR++++ETP NP + + DI A++ L + A Sbjct: 125 HHGLGRFGVTVRHVDMTDPARVAEALTAKTRVLYLETPANPNMRLVDIAAVSALAHAQGA 184 Query: 179 KVLVDNTFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAF--LQ 236 KV+VDNT+ +P LQQPL LGADV +HS TKY+GGH D+ GA V D EL + L+ Sbjct: 185 KVVVDNTYCTPYLQQPLLLGADVSVHSMTKYLGGHGDLTAGAAVFADAELAQRVRLYGLK 244 Query: 237 NGAGAVPGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGH 296 + GAV DA+L MRGLKTL LRM RH ++A VAEF+A HP+ ++V YPGLPS H Sbjct: 245 DMTGAVMSAQDAHLVMRGLKTLALRMDRHCQSAQKVAEFIAAHPAAAAVHYPGLPSFAQH 304 Query: 297 EIAARQMRGFGGMVSVRMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTA 356 +A +QMR GGM++ +R G +A ++ A SLG E+L +HP++MTH++ Sbjct: 305 ALAKQQMRQMGGMIAFELRGGLQAGVRFMDALQLVTRAVSLGDAETLAQHPASMTHSTYT 364 Query: 357 GSQLE---VPDDLVRLSVGIEDIADLLGDLEQAL 387 Q + + LVRLSVG+ED+ DLL D+ QAL Sbjct: 365 PEQRAAHGIAEGLVRLSVGLEDLDDLLADIGQAL 398 Lambda K H 0.319 0.135 0.393 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: 495 Number of extensions: 27 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: 388 Length of database: 434 Length adjustment: 31 Effective length of query: 357 Effective length of database: 403 Effective search space: 143871 Effective search space used: 143871 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 (21.7 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