Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate CCNA_00553 CCNA_00553 hydroxyacylglutathione hydrolase
Query= curated2:Q0AM20 (256 letters) >FitnessBrowser__Caulo:CCNA_00553 Length = 249 Score = 266 bits (681), Expect = 2e-76 Identities = 144/253 (56%), Positives = 167/253 (66%), Gaps = 8/253 (3%) Query: 4 LLIRQFPCLSDNYGFLIHDPDSGETATIDTPDADVILNEADQAGWSITQIWNTHHHFDHA 63 L + QF CLSDNYGFL+ D SG+ ATIDTPDA IL E + GWS+ I NTH H DHA Sbjct: 3 LTVHQFRCLSDNYGFLVRDEASGKVATIDTPDAGAILAELAKLGWSLDLILNTHWHPDHA 62 Query: 64 GGNETIQALTGAKVVAPRYDRHRIPGISMEVEDGDVISLGDHKAKVFYTPGHTMGHVCYH 123 GGNET++ TGA +V P + RI + V DG+ + LGD + V T GHT+GHV Y+ Sbjct: 63 GGNETLKTATGATIVGPA-EVTRIAPLDRVVRDGEEVMLGDTRLTVIDTGGHTLGHVSYY 121 Query: 124 MPMDGIAFVGDTLFALGCGRLFEGTPAEMWHSLSRLAALPDETRIYCAHEYTEANARFAL 183 D IAFVGDTLFALGCGRLFEGT +MW SL RL ALPDET +YCAHEYT +NARFAL Sbjct: 122 DAEDAIAFVGDTLFALGCGRLFEGTAEQMWDSLGRLIALPDETTVYCAHEYTASNARFAL 181 Query: 184 SIDPDNHDLQVYAAMVEGERARGEPTVPTTIAAEKAANPFLRPDDPAIRARLGMEHDDDE 243 S+D + L A V RAR E TVPTTI EKA NPFLR P +R + Sbjct: 182 SVD-SSAALAARAEAVFAARARDEATVPTTIGVEKATNPFLRA--PLLRP----DAPSPA 234 Query: 244 EVFAEIRRRKDSF 256 + FAEIR KDSF Sbjct: 235 QAFAEIRAAKDSF 247 Lambda K H 0.320 0.137 0.426 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: 253 Number of extensions: 8 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: 256 Length of database: 249 Length adjustment: 24 Effective length of query: 232 Effective length of database: 225 Effective search space: 52200 Effective search space used: 52200 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: 46 (22.3 bits)
Align candidate CCNA_00553 CCNA_00553 (hydroxyacylglutathione hydrolase)
to HMM TIGR03413 (gloB: hydroxyacylglutathione hydrolase (EC 3.1.2.6))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR03413.hmm # target sequence database: /tmp/gapView.25691.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03413 [M=248] Accession: TIGR03413 Description: GSH_gloB: hydroxyacylglutathione hydrolase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-89 283.8 0.0 6.4e-89 283.6 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00553 CCNA_00553 hydroxyacylglutathion Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00553 CCNA_00553 hydroxyacylglutathione hydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.6 0.0 6.4e-89 6.4e-89 1 248 [] 5 247 .. 5 247 .. 0.97 Alignments for each domain: == domain 1 score: 283.6 bits; conditional E-value: 6.4e-89 TIGR03413 1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfpvkvv 72 ++++++lsdNy +l++de+s +++ +D+++a +l+ l++ g++l+ il+TH+H DH gg+++l++++++++v lcl|FitnessBrowser__Caulo:CCNA_00553 5 VHQFRCLSDNYGFLVRDEASgKVATIDTPDAGAILAELAKLGWSLDLILNTHWHPDHAGGNETLKTATGATIV 77 6899****************9**************************************************** PP TIGR03413 73 gpaee.ripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqm 144 gpae ri+ l++ v++g+ev l++++++v+++ GHtlgH++yy +e+ + F+gDtLf++GCGrlfegtaeqm lcl|FitnessBrowser__Caulo:CCNA_00553 78 GPAEVtRIAPLDRVVRDGEEVMLGDTRLTVIDTGGHTLGHVSYYDAEDAIAFVGDTLFALGCGRLFEGTAEQM 150 ***999******************************************************************* PP TIGR03413 145 leslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLr 217 ++sl +l aLp+et+vycaHEYt+sN+rFal+v++ ++al++r+++v a+ra++++t+P+t++ ekatNpFLr lcl|FitnessBrowser__Caulo:CCNA_00553 151 WDSLGRLIALPDETTVYCAHEYTASNARFALSVDS-SAALAARAEAVFAARARDEATVPTTIGVEKATNPFLR 222 *********************************97.789********************************** PP TIGR03413 218 aeeaevkaaleeekaeevevfaelRekkdkf 248 a + ++ +++++fae+R++kd+f lcl|FitnessBrowser__Caulo:CCNA_00553 223 APLLRP------DAPSPAQAFAEIRAAKDSF 247 987666......678899***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (249 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.72 // [ok]
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