Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_164928286.1 BL_RS08165 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000007525.1:WP_164928286.1 Length = 410 Score = 236 bits (603), Expect = 7e-67 Identities = 154/399 (38%), Positives = 211/399 (52%), Gaps = 24/399 (6%) Query: 12 DRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFE------YSRTHNPT 65 D+ L TLAIH G D TGA+ PI + YA + Y+R +P Sbjct: 14 DQPLGFGTLAIHLGNGVDAETGAIRRPITLANAYALPYDPSDINWSSSDVNLYTRNGHPN 73 Query: 66 RFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRR 124 + E +A LEG A ASG+AA +T L+ G H + D Y +RL ++ Sbjct: 74 QRYLEEKLARLEGAEDAVVLASGVAALAATFTTFLNRGDHAIFSDTTYIAAYRLLNQILP 133 Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHG--LLT 182 G++ S +D +DP +AA+R +TK+V IETP NP LK+ DIA IA +A + +L Sbjct: 134 EKYGIETSILDTSDPENVRAALRPNTKLVHIETPANPTLKVSDIATIAKLAHEANPDILV 193 Query: 183 VVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSI 242 VDNTF +P RPL+LGAD+V+ S TKY+NGH D +GG ++ A + Q + Sbjct: 194 SVDNTFNTPYNVRPLNLGADIVIESLTKYINGHGDALGG-SIATTKARTDQIRFTAQVNF 252 Query: 243 GGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLA 302 GG+ PF+++L RG TLPLR+R H ALA+A+ LE+ + V YPGL SHP H +A Sbjct: 253 GGIISPFNAWLINRGSVTLPLRIRQHNALALAIAKHLESLDVVRFVAYPGLESHPHHEVA 312 Query: 303 KRQM----SGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLV---NHPAVMTH 355 Q+ SGFGG++S L D RF K + T A SLG ESL+ + Sbjct: 313 VSQLARPDSGFGGVLSFGLDTNHDGHNRFVSKLNVITSAVSLGHDESLIVFLGEDDERQY 372 Query: 356 ASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERALV 394 P R RL+VG+ED DL D++ ALV Sbjct: 373 LYPPEFHR-------GFFRLAVGLEDTDDLIRDIDHALV 404 Lambda K H 0.320 0.134 0.391 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: 446 Number of extensions: 24 Number of successful extensions: 7 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: 397 Length of database: 410 Length adjustment: 31 Effective length of query: 366 Effective length of database: 379 Effective search space: 138714 Effective search space used: 138714 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 12 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