Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate Ga0059261_1388 Ga0059261_1388 cystathionine beta-lyase, bacterial
Query= reanno::acidovorax_3H11:Ac3H11_2452 (415 letters) >FitnessBrowser__Korea:Ga0059261_1388 Length = 411 Score = 159 bits (401), Expect = 2e-43 Identities = 130/412 (31%), Positives = 191/412 (46%), Gaps = 43/412 (10%) Query: 11 TQIVHADRLGGAEQGAIHQPIHTSVQYGYDKVEDLIAVFQGTAKGGFNYARQGTPTTAAL 70 T++V A R QG ++ P+ + YD V DL A Y R+G+PT +L Sbjct: 26 TRVVGAGRRPEWTQGIVNAPVWRASTILYDTVADLRASAGSDTHHRLFYGRRGSPTQWSL 85 Query: 71 EAKITKMERG-HGTIVFSSGMAGICAVFLTLLKAGDHLVASQFVFGNTNS-VLGTLADLG 128 +T++E G T ++ SG+A + A L++L GD L+ + V+ T S G L G Sbjct: 86 AEALTELEPGAEATFLYPSGVAAVSAALLSVLSPGDELLLADSVYDPTRSFATGFLKRFG 145 Query: 129 VEVTTVDVTDAANVAAALRPNTRMVFVETIANPGTQIPDLEGIGALCKAHGALYVVDNTV 188 V D A +A + TR +F+ET + ++ D+ I A KA G + ++DNT Sbjct: 146 VITRFYDPMIGAGIAELITDKTRAIFMETPGSLTFEVQDVPAIVAAAKARGVVTLLDNTW 205 Query: 189 ASPYLFRAATVGAGLVVNSLTKSIGGLGDALGGAITDTGLYDWSRYPNIFAAYRKGDAKG 248 A+P LF A G L + + TK + G D + G++T T A+ Sbjct: 206 ATPLLFPAIEKGIDLSILACTKYVVGHSDVMLGSVTAT-------------------AEH 246 Query: 249 WGLQQLRKKGLRDMGGTLSSHAAHQLALGAETLALRMDRTSATALALAQWLEAHPAIARV 308 W QQLR +G T S A + G T+ALR+ + AL +A+WLE P +ARV Sbjct: 247 W--QQLRATSFA-LGQTASPDDAWLGSRGLRTMALRLKQHGEAALEIARWLETRPEVARV 303 Query: 309 HYPLLPSHPQHAFAKKHLKAGSWLLSFELRDPDQC--LPVCNRLQLPIKATGLADTRTLI 366 +P LPS P H + K + L SF LR ++ + + L+L +L Sbjct: 304 LHPALPSCPGHDLFVRDFKGPAGLFSFVLRGGNEAGRAALIDSLELFGIGYSWGGFESLA 363 Query: 367 IPV-----AHTIFWEA-GPAVRASMGIADSMIRLSVGLEEVEDLLADFEQAL 412 IPV I W+A GPAV RL +GLE+ DL+AD L Sbjct: 364 IPVDPDRIRTVIPWQAEGPAV-----------RLQIGLEDPADLIADLAAGL 404 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: 384 Number of extensions: 22 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: 411 Length adjustment: 31 Effective length of query: 384 Effective length of database: 380 Effective search space: 145920 Effective search space used: 145920 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