Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate PP_0659 PP_0659 Cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Putida:PP_0659 Length = 423 Score = 273 bits (697), Expect = 9e-78 Identities = 160/392 (40%), Positives = 221/392 (56%), Gaps = 12/392 (3%) Query: 10 DGDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQS--------SPGEHQGFEYSRT 61 +G+ A + T + G+ A PI ++ Y + + G+ GF YSR Sbjct: 8 EGNAAAGVGTRVVWSGEQVQHPYNATQTPIVVSAAYGYNDIDAWYDVAQGKQPGFIYSRM 67 Query: 62 HNPTRFAYERCVAALEGGTRAFAFASGMAATSTVME-LLDAGSHVVAMDDLYGGTFRLFE 120 NPT E +A LE A AF+SGMAA S V+ L G VV+ D YGGT ++FE Sbjct: 68 SNPTVATLEAKLAELEQAESAVAFSSGMAAISAVLHTFLSNGKRVVSTRDSYGGTNKIFE 127 Query: 121 RVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGL 180 R G+ D D A + I A ++++ETPTNP LK++DI ++ A K G Sbjct: 128 EFLPRM-GVQVCLCDTLDTEALEREIAAGCDLLYLETPTNPTLKVLDIRRLSAAAHKVGA 186 Query: 181 LTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQN 240 L V DNTFA+P+ Q PL+LG D+VVHSATK+L+GH D++GG+ V G A +A Q+ + Sbjct: 187 LVVADNTFATPLNQNPLALGVDVVVHSATKFLSGHGDVLGGV-VCGAEALMA-QVRHYRE 244 Query: 241 SIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHV 300 G PF ++L +RG+KTL +R+R +A+ALA +L T P +E V YPGL +H H Sbjct: 245 INGAALDPFSAYLIIRGIKTLAVRLRQQQASAMALAHYLSTEPLVEAVNYPGLPAHAGHA 304 Query: 301 LAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPV 360 +AK QM GFG IVS VLKGG R + + A +LG VE++ +H + Sbjct: 305 IAKAQMRGFGAIVSFVLKGGMPTVARLLPRLKYAHRAGNLGAVETIYGPARTTSHVENTL 364 Query: 361 ARREQLGISDALVRLSVGIEDLGDLRGDLERA 392 R LGIS+ LVR+SVGIE+ DL DL +A Sbjct: 365 EERLALGISEGLVRISVGIEETDDLLADLAQA 396 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: 430 Number of extensions: 23 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: 397 Length of database: 423 Length adjustment: 31 Effective length of query: 366 Effective length of database: 392 Effective search space: 143472 Effective search space used: 143472 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