Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_012043307.1 BBTA_RS14845 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000015165.1:WP_012043307.1 Length = 431 Score = 276 bits (707), Expect = 7e-79 Identities = 164/427 (38%), Positives = 236/427 (55%), Gaps = 14/427 (3%) Query: 1 MNDKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGR 60 M K F T LH+ +Q G+ PI+ + ++ ++D A +F ++ G+ Y R Sbjct: 1 MPPPKPPAFETLSLHAGQQPDPATGARAVPIYQTTSYVFDDTEHAAALFNLERAGHIYTR 60 Query: 61 QGNPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNT-NSL 119 NPT A LE+++ +E G IC A+G AA+ + LL GDH+V+S+ L+G T N L Sbjct: 61 ISNPTTAVLEERLAALEGGVGAICTASGQAALHLAIATLLNAGDHIVASSSLYGGTINLL 120 Query: 120 WMTVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGI 179 T+ G S V D+ AAI T+LV ET+ NP +V D+ RI + E GI Sbjct: 121 AHTLPRFGITTSFVKPRDLDGFRAAIQPKTKLVIGETLGNPGLEVLDIPRISAIAHEAGI 180 Query: 180 LYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHI 236 ++DNT +PYL +P GA +V++S TK +GGHG A+GGA+ D G FDW ++P + Sbjct: 181 PLLIDNTFATPYLSQPIAQGADIVMHSATKWLGGHGIAIGGAIIDGGRFDWRASGKFPQL 240 Query: 237 AENY--------KKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQEREC 288 E Y + P + + R + LRDFG L P A H+ G ET+ LR ER Sbjct: 241 TEPYAGYHGIVFDEQFGPAAFIMRARTEGLRDFGACLSPTNAFHLLQGVETLHLRMERHV 300 Query: 289 KNALALAQMLQADERVAAVYYPGLESHPQHALSKALF-RSFGSLMSFELKDGIDC-FDYL 346 N A+ L A++ V V +P LE+HP HAL+K L R GS++SF +K G ++ Sbjct: 301 ANTSAVLAALTANKAVDWVLHPSLETHPDHALAKQLLPRGAGSIISFGIKGGRPAGRKFI 360 Query: 347 NRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVAD 406 L+L +N+GD +TLVI A T +M A + A+ GI E LIR+SVG+E D++ D Sbjct: 361 ESLKLISHLANVGDAKTLVIHPASTTHQQMDAAQLAAAGIGEELIRLSVGIEAVSDIIDD 420 Query: 407 FRQALDA 413 QAL A Sbjct: 421 LGQALRA 427 Lambda K H 0.319 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: 467 Number of extensions: 18 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: 413 Length of database: 431 Length adjustment: 32 Effective length of query: 381 Effective length of database: 399 Effective search space: 152019 Effective search space used: 152019 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 10 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