Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 3607379 Dshi_0793 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)
Query= BRENDA::E9AFE7 (409 letters) >FitnessBrowser__Dino:3607379 Length = 431 Score = 226 bits (575), Expect = 1e-63 Identities = 152/422 (36%), Positives = 211/422 (50%), Gaps = 40/422 (9%) Query: 22 SQGFDTLQVHAGVRPDPVTGAILTPIYQSTTFV------QESINSYQAKGYSYTRSANPT 75 S GFDTLQ+HAG RPDP TGA TPIYQ+T +V ++ + Q GY Y+R NPT Sbjct: 7 SYGFDTLQIHAGARPDPATGARQTPIYQTTGYVFRDADHAAALFNLQEVGYIYSRLTNPT 66 Query: 76 VAVLEQKLCALENGSYCTVYNTGMAATTTAISSFMNAGDHAILTNCCYGGTNRACRVFFS 135 VAVL++++ LE G ++G AA A+ M G + +++ YGGT Sbjct: 67 VAVLQERIATLEGGVGAVCCSSGHAAQIMALFPLMQPGCNIVVSTRLYGGTVTQFGQTIK 126 Query: 136 RLGMEFTFVDMRDPQNVIDSIKPNTKLVISETPANPTLILIDVAAVSKICKERGIVHMCD 195 R G FVD D V +I +T+ V E ANP ++DV A++ I GI + D Sbjct: 127 RFGWSAKFVDFDDLDAVRAAIDDDTRAVFGEAIANPGGYIMDVRAIADIADAAGIPLIID 186 Query: 196 NTFATAYIMRPLDHGADVTLISTTKYVDGHDMTVGGALVTNSK----------------- 238 NT AT Y+ RP++HGA + + STTKY+ G+ GG +V + K Sbjct: 187 NTTATPYLCRPIEHGATLVVHSTTKYLTGNGTVTGGCVVDSGKFDWAASGKFPSLSEPEP 246 Query: 239 --------ELDAKVRLT-------QNILGNVMSPQVAFLQLQTVKTMSLRVTKQSHNAQK 283 E + T LG M+PQ A L ++T+SLR+ + NA+K Sbjct: 247 AYHGLRFAETFGPLAFTFHGIAVGLRDLGMTMNPQGAHYTLMGIETLSLRMARHVENAEK 306 Query: 284 IAEFLETHRAVDRVVYPGLASHPQKELADRQHRNNLHGGMLWFEVKGGTAAGRRLMDTVP 343 IA++LE V+ V Y GL S P E G + F VKGG A +L+D++ Sbjct: 307 IAKWLEADDRVEFVTYAGLPSSPYFERVKTVCPRGA-GALFTFAVKGGYEACIKLVDSL- 364 Query: 344 RPWSLCENLGASESIITCPSVMTHANMTSEDRMKVGITDGFVRVSCGIEDVDDLIAALKV 403 +S NLG + S+I + TH +T E + G VR+S GIED DDLIA L Sbjct: 365 EIFSHVANLGDTRSLIIHSASTTHRQLTPEQQEAAGAAPNVVRLSIGIEDADDLIADLDQ 424 Query: 404 AM 405 A+ Sbjct: 425 AL 426 Lambda K H 0.319 0.132 0.388 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: 474 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 409 Length of database: 431 Length adjustment: 32 Effective length of query: 377 Effective length of database: 399 Effective search space: 150423 Effective search space used: 150423 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