Align lactoylglutathione lyase (EC 4.4.1.5) (characterized)
to candidate SMc01961 SMc01961 hypothetical protein
Query= BRENDA::Q9CJC0 (389 letters) >FitnessBrowser__Smeli:SMc01961 Length = 317 Score = 211 bits (537), Expect = 2e-59 Identities = 131/351 (37%), Positives = 186/351 (52%), Gaps = 42/351 (11%) Query: 14 NLTLGGVHHVTAITSSAQKIYDFFTNILGLRLAKLTVNQDDYETYHLFFTEEDGH-GADM 72 +L L G+HH+TAIT++A + F+T LGLRL K TVNQDD YHLF+ + G D+ Sbjct: 2 SLQLTGIHHLTAITANAPENLRFYTGTLGLRLVKKTVNQDDTTAYHLFYADGQATPGTDL 61 Query: 73 TFFDFKDIPKGNHGVNNIERASFRVPTDASLDYWTRRFDNAHVKHGEISSKFGQKTLEFE 132 TFFD+ + + G ++I R RV + ++ +W RFD V GE++ G+ +L+FE Sbjct: 62 TFFDWP-VGREGRGTHSISRTGLRVGSAETVRWWKSRFDELEVASGEVAEIDGRASLDFE 120 Query: 133 DFDGQLYQLISDQNNSGDDSKGRSWQLSNVPQEHGITGLGPVFVKVENAENLRTILETVF 192 D +GQ ++L+ D G + W+ S VP EH I GLGP+ + V + N +L V Sbjct: 121 DGEGQRFRLVDD----GGLAPSHPWERSPVPSEHQIKGLGPITISVPDISNTALVLTRVM 176 Query: 193 GFR----YAGQED--DLHLFEVANGGNGAALILQEAGEKEAYAYQGYGTIHHLALGTANP 246 Y + ++H+F + +GG A L + + A A QG G +HH+A + Sbjct: 177 NMAELRSYPSPDGVGEVHVFSMGDGGPAAELHVAVQPDLPA-ARQGAGAVHHVAFRAPDV 235 Query: 247 ETLNYWIERIKAFRLPHSGLVDRFYFSSEYVRVAPGVLFEIATYTPGIGALDMAKSGLGA 306 E L+ W ER+ FRLP SG V+RFYF S Y R G+LFEIAT P Sbjct: 236 EALHRWTERLGEFRLPSSGEVERFYFRSLYFREPNGILFEIATDGP-------------- 281 Query: 307 VDSYEEALITSGFWIDQTKEESGLSLSLPPHLFPGDEATKARTAASLRPLD 357 GF +D+ E G SLSLPP L E +A+ A L+PL+ Sbjct: 282 -----------GFAVDEPMETLGESLSLPPFL----EPKRAQIEARLKPLE 317 Score = 42.0 bits (97), Expect = 2e-08 Identities = 25/134 (18%), Positives = 52/134 (38%) Query: 11 IPENLTLGGVHHVTAITSSAQKIYDFFTNILGLRLAKLTVNQDDYETYHLFFTEEDGHGA 70 +P + G+ +T T ++ + + + D H+F + G A Sbjct: 146 VPSEHQIKGLGPITISVPDISNTALVLTRVMNMAELRSYPSPDGVGEVHVFSMGDGGPAA 205 Query: 71 DMTFFDFKDIPKGNHGVNNIERASFRVPTDASLDYWTRRFDNAHVKHGEISSKFGQKTLE 130 ++ D+P G + +FR P +L WT R + +F ++L Sbjct: 206 ELHVAVQPDLPAARQGAGAVHHVAFRAPDVEALHRWTERLGEFRLPSSGEVERFYFRSLY 265 Query: 131 FEDFDGQLYQLISD 144 F + +G L+++ +D Sbjct: 266 FREPNGILFEIATD 279 Lambda K H 0.316 0.135 0.399 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: 352 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 389 Length of database: 317 Length adjustment: 29 Effective length of query: 360 Effective length of database: 288 Effective search space: 103680 Effective search space used: 103680 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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