Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_041098967.1 SUTH_RS09960 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000828635.1:WP_041098967.1 Length = 427 Score = 255 bits (652), Expect = 2e-72 Identities = 154/422 (36%), Positives = 225/422 (53%), Gaps = 14/422 (3%) Query: 6 TYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPT 65 TY F T LH+ + +G+ PI+ + +F ++D+ Q A +F ++ G+ Y R NPT Sbjct: 2 TYNFDTLALHAGQVPDERYGARATPIYLTTSFVFKDSDQAAALFNMERAGHVYSRISNPT 61 Query: 66 VAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLW-MTVG 124 A LE++I +E G I A+G AA+ + L+ G H+V+S L+G +++L T+ Sbjct: 62 NAVLEERIAALEGGVGAIAVASGQAALHLAIATLMGAGSHIVASRSLYGGSHNLLDYTLP 121 Query: 125 AQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVD 184 G + VD D+ AAI TRL+F ET+ NP V ++ + L E G+ +VD Sbjct: 122 RFGITTTFVDPRDLDAWRAAIRPETRLLFGETLGNPGLDVLNIPEVAALAHEHGLPLMVD 181 Query: 185 NTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT---RYPHIAENYK 241 +T T+P+L RP GA L+ +S TK +GGHG A+GG L D G FDW ++P + E Y+ Sbjct: 182 STFTTPWLMRPFDHGADLIFHSATKFLGGHGVAIGGLLVDGGTFDWDKSGKFPTLTEPYE 241 Query: 242 KNPAPQWG--------MAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALA 293 + + + R + LRDFG + P A + G ET+ LR ER N Sbjct: 242 GFHGMDFSEESTVAAFLLRARREGLRDFGACMSPMTAFQLLQGVETLPLRMERHIANTRQ 301 Query: 294 LAQMLQADERVAAVYYPGLESHPQHALS-KALFRSFGSLMSFELKDGIDC-FDYLNRLRL 351 L E VA V YP LE+HP HAL+ K L R GS+ SF LK G ++ LR+ Sbjct: 302 AVAHLVKHEAVAGVGYPELENHPDHALAQKLLPRGAGSVFSFTLKGGRAAGRKFIEALRV 361 Query: 352 AIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQAL 411 +N+GD ++LVI A T + M + GI IR+S+GLED DL+ D + L Sbjct: 362 FSHLANVGDAKSLVIHPASTTHFRMSDAALVAAGIHPGTIRLSIGLEDAGDLIEDLNRGL 421 Query: 412 DA 413 A Sbjct: 422 AA 423 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: 472 Number of extensions: 27 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: 427 Length adjustment: 32 Effective length of query: 381 Effective length of database: 395 Effective search space: 150495 Effective search space used: 150495 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