Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate SMc01976 SMc01976 hypothetical protein
Query= BRENDA::Q1M0P5 (380 letters) >FitnessBrowser__Smeli:SMc01976 Length = 390 Score = 233 bits (593), Expect = 9e-66 Identities = 144/371 (38%), Positives = 212/371 (57%), Gaps = 17/371 (4%) Query: 20 AVSVPIYQTSTYR----QDAIGHHKGYE----YSRSGNPTRFALEELIADLEGGVKGFAF 71 AV PI QTS + + + ++G Y+R NPT EE++A LEG F Sbjct: 25 AVVPPIVQTSLFTFKDYDEMVASYRGERVRPIYTRGLNPTVRHFEEMLAKLEGAEDAIGF 84 Query: 72 ASGLAGIHA-VFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIIDTSDLSQIKKA 130 ASG++ I + V S ++ GD ++ VY FRLF L + + T +D D + KA Sbjct: 85 ASGMSAISSTVLSFVEPGDRIVAVKHVYPDAFRLFGTHLKRMRVEVTYVDGRDEEAVAKA 144 Query: 131 IKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQNPLLLGADIVV 190 + P K Y+E+P++ ++ D+A A++A+ G++T++DN++A+P +Q P+ LG D+V+ Sbjct: 145 L-PGAKLFYMESPTSWVMDTHDVAALAALARRQGIVTVIDNSWASPVFQQPVSLGVDLVI 203 Query: 191 HSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQRGIKTLGLRMQ 250 HS +KYLGGHSDVVAG+V + E + + + +GG L P D+WLL RG++TL +RM+ Sbjct: 204 HSASKYLGGHSDVVAGVVAGSGELIGRIRSEAYPYLGGKLSPFDAWLLIRGMRTLPVRMK 263 Query: 251 AHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSFTLKNDSEATPF 310 AH+++AL VA L +HP VE V +PGL H + G SG+ SF + + F Sbjct: 264 AHERSALAVARRLAEHPLVETVCHPGLGNH-----LPPGLSGTSGLFSFIFREGVDVRRF 318 Query: 311 VESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAA-GIRDGLVRLSVGIEHEQDLL 369 + LKLF LG S GG ESL+ VP + A + AA GI VRL VG+E + L Sbjct: 319 ADHLKLFKLGVSWGGHESLI-VPGEVVLAQKAEPNSAAAFGISPRSVRLHVGLEGTEALW 377 Query: 370 EDLEQAFAKIS 380 DLE A S Sbjct: 378 SDLEAAMTAAS 388 Lambda K H 0.318 0.136 0.394 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: 359 Number of extensions: 16 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: 380 Length of database: 390 Length adjustment: 30 Effective length of query: 350 Effective length of database: 360 Effective search space: 126000 Effective search space used: 126000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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