Align Cystathionine gamma-synthase 1, chloroplastic; AtCGS1; METHIONINE OVERACCUMULATION 1; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate GFF2323 PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ
Query= SwissProt::P55217 (563 letters) >FitnessBrowser__Phaeo:GFF2323 Length = 396 Score = 243 bits (620), Expect = 1e-68 Identities = 140/385 (36%), Positives = 217/385 (56%), Gaps = 9/385 (2%) Query: 180 VHAGERLGRGIVTDAITTPVVNTSAYFFKKTAELID--FKEKRSVSFEYGRYGNPTTVVL 237 VH G R + + ++ + T + + TAE + F E F Y RYGNPT + Sbjct: 12 VHGGTRRSQ---YNEVSEAIYLTQGFVYD-TAEQAEARFIETGPDEFIYARYGNPTVAMF 67 Query: 238 EDKISALEGAESTLVMASGMCASTVMLLALVPAGGHIVTTTDCYRKTRIFMENFLPKLGI 297 E++I+ALEGAE ASGM A L +++ AG H+V+ + +EN L + G+ Sbjct: 68 EERIAALEGAEDAFATASGMAAVNGALTSILKAGDHVVSAKALFGSCLYILENILTRYGV 127 Query: 298 TVTVIDPADIAGLEAAVNEFKVSLFFTESPTNPFLRCVDIELVSKICHKRGTLVCIDGTF 357 VT +D D+ AA+ ++FF ES +NP L +DI V+++ H G V +D F Sbjct: 128 EVTFVDGTDLDAWRAALRPDTKAVFF-ESMSNPTLEVIDIAAVAELAHAVGATVVVDNVF 186 Query: 358 ATPLNQKALALGADLVVHSATKYIGGHNDVLAGCICGSLKLV-SEIRNLHHVLGGTLNPN 416 +TP+ A+ GAD+V++SATK+I G VL G I G+ + + GG+L+P Sbjct: 187 STPVFSNAIEQGADVVIYSATKHIDGQGRVLGGVILGTRDFIRGTVEPYMKHTGGSLSPF 246 Query: 417 AAYLIIRGMKTLHLRVQQQNSTAFRMAEILEAHPKVSHVYYPGLPSHPEHELAKRQMTGF 476 A+ +++G++T+ LRV Q TA +A+ L HP +S + YPGL H +H L +RQ+ G Sbjct: 247 NAWTLLKGLETISLRVNAQAETALELAQALSGHPALSRLMYPGLEDHAQHALVQRQLGGK 306 Query: 477 GG-VVSFEIDGDIETTIKFVDSLKIPYIAPSFGGCESIVDQPAIMSYWDLPQEERLKYGI 535 GG V+S ++ G + +F+++L IP I+ + G +SI PA ++ L +E + + GI Sbjct: 307 GGTVLSLDLKGGKDAAFRFLNALTIPVISNNLGDAKSIATHPATTTHQRLSEELKSELGI 366 Query: 536 KDNLVRFSFGVEDFEDVKADILQAL 560 LVRFS G+ED D+ AD+ QAL Sbjct: 367 TPGLVRFSVGLEDAGDLIADLTQAL 391 Lambda K H 0.318 0.132 0.379 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: 419 Number of extensions: 13 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: 563 Length of database: 396 Length adjustment: 33 Effective length of query: 530 Effective length of database: 363 Effective search space: 192390 Effective search space used: 192390 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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