Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_012383819.1 BIND_RS04130 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::acidovorax_3H11:Ac3H11_2452 (415 letters) >NCBI__GCF_000019845.1:WP_012383819.1 Length = 427 Score = 221 bits (562), Expect = 4e-62 Identities = 150/418 (35%), Positives = 219/418 (52%), Gaps = 14/418 (3%) Query: 9 FTTQIVHADRLGGAEQGAIHQPIHTSVQYGYDKVEDLIAVFQGTAKGGFNYARQGTPTTA 68 F+T VHA GA PI+ + + ++ + A F G + G Y+R PT A Sbjct: 10 FSTLAVHAGAAPDPTTGARVTPIYQTTSFVFENADQAAARF-GLQEFGNIYSRITNPTNA 68 Query: 69 ALEAKITKMERGHGTIVFSSGMAGICAVFLTLLKAGDHLVASQFVFGNT-NSVLGTLADL 127 LE +I +E G + +SG A VF TLL+ G+ ++A+ ++G + N + + Sbjct: 69 VLEERIAALEGGTAALAVASGHAAQLLVFHTLLQPGETILAATKLYGGSINQLSHAFKNF 128 Query: 128 GVEVTTVDVTDAANVAAALRPNTRMVFVETIANPGTQIPDLEGIGALCKAHGALYVVDNT 187 G VT D D AAA+ P T+ +FVE+IANPG I DLE I + K H VVDNT Sbjct: 129 GWGVTFADTDDLKAFAAAVTPQTKAIFVESIANPGGTITDLEAIANIAKTHKIPLVVDNT 188 Query: 188 VASPYLFRAATVGAGLVVNSLTKSIGGLGDALGGAITDTGLYDW--SRYPNIFAAYRKGD 245 +ASPYL R GA ++V+S TK +GG G+++GG I D G +DW RYP + A + + Sbjct: 189 LASPYLVRPFEHGADIIVHSATKFLGGQGNSMGGLIVDGGTFDWRDPRYPMLSAPHAEYG 248 Query: 246 ----AKGWG----LQQLRKKGLRDMGGTLSSHAAHQLALGAETLALRMDRTSATALALAQ 297 A+ +G R GLRD+G LS A L G ETL LRM R S AL +A Sbjct: 249 GLVIAETFGNIAFALAARALGLRDLGPALSPFNAFLLLNGIETLPLRMQRHSDNALIVAT 308 Query: 298 WLEAHPAIARVHYPLLPSHPQHAFAKKHLKAGSW-LLSFELRDP-DQCLPVCNRLQLPIK 355 L H + V Y LP + A+K+ G+ + +F + D L + L+L Sbjct: 309 HLAQHHKVDWVSYAGLPGDRYYELARKYSPLGAGAVFTFGVHGGYDAALKTVSSLKLFSL 368 Query: 356 ATGLADTRTLIIPVAHTIFWEAGPAVRASMGIADSMIRLSVGLEEVEDLLADFEQALA 413 + DTR+L+I A T + A + + G ++R+S+G+E+V D++AD +QALA Sbjct: 369 LANVGDTRSLVIHPASTTHRQLTDAQKIAAGAGPEVVRVSIGIEDVRDIIADLDQALA 426 Lambda K H 0.320 0.134 0.398 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: 442 Number of extensions: 26 Number of successful extensions: 5 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: 415 Length of database: 427 Length adjustment: 32 Effective length of query: 383 Effective length of database: 395 Effective search space: 151285 Effective search space used: 151285 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