Align Hydroxyacylglutathione hydrolase; EC 3.1.2.6; Glyoxalase II; Glx II (uncharacterized)
to candidate WP_043747124.1 AMB_RS21210 hydroxyacylglutathione hydrolase
Query= curated2:Q60BX0 (256 letters) >NCBI__GCF_000009985.1:WP_043747124.1 Length = 257 Score = 312 bits (800), Expect = 4e-90 Identities = 153/250 (61%), Positives = 181/250 (72%), Gaps = 1/250 (0%) Query: 6 QIPVLEDNYVYLLHEPGSGATAAVDPAVAGPVLEALDARGWRLGHVLNTHHHGDHVGGNL 65 QIPVL DNYVYL HEP GATAA+DPAV+ PVLE L ARGW L H+LNTHHHGDH G NL Sbjct: 8 QIPVLSDNYVYLAHEPLGGATAAIDPAVSEPVLERLAARGWTLTHILNTHHHGDHTGANL 67 Query: 66 ELKAATGCTVVGAAGDRHRIPGIDVALKDGEEFRLGSASARMLDVPGHTSGHVAFWFEDD 125 +L TGC VVGAA D RIPGI + + +GE F LG A+ +L+VPGHTSGHVA+W D Sbjct: 68 DLARRTGCAVVGAARDSERIPGITLEVSEGETFMLGHAAVTVLEVPGHTSGHVAYWLADS 127 Query: 126 AALFCGDTLFALGCGRLFEGSAEQMWRSLERLRALPAETKVFCAHEYTQANARFAVTIEP 185 LFCGDTLF+LGCGRLFEG+AE+MW SL++LR LP +T + AHEYT N RFA +E Sbjct: 128 HVLFCGDTLFSLGCGRLFEGTAEEMWASLKKLRDLPPDTLAYPAHEYTAGNGRFARLVER 187 Query: 186 GNAALRERVERVEALRREGAATVPSILSEELATNPFLRPESPEIRARLGL-PGVPEVEVF 244 N AL+ R++ VE LR TVP L++E A NPFLR ++ I +GL PG VF Sbjct: 188 DNGALKARLDEVERLRAHNRPTVPVRLADERAANPFLRADTAAIARAVGLEPGTDPALVF 247 Query: 245 AEIRRRKDVF 254 AE+RRRKDVF Sbjct: 248 AELRRRKDVF 257 Lambda K H 0.321 0.138 0.418 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: 260 Number of extensions: 5 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 232 Effective length of database: 233 Effective search space: 54056 Effective search space used: 54056 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: 47 (22.7 bits)
Align candidate WP_043747124.1 AMB_RS21210 (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.29106.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-100 321.9 0.0 1.5e-100 321.7 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_043747124.1 AMB_RS21210 hydroxyacylglutathio Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_043747124.1 AMB_RS21210 hydroxyacylglutathione hydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 321.7 0.0 1.5e-100 1.5e-100 1 248 [] 6 257 .] 6 257 .] 0.99 Alignments for each domain: == domain 1 score: 321.7 bits; conditional E-value: 1.5e-100 TIGR03413 1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfp 68 +++ip+lsdNy++l +++ +++++Dp+ +epvle l+++g++l++il+THhH DH+g++ +l ++++ lcl|NCBI__GCF_000009985.1:WP_043747124.1 6 VEQIPVLSDNYVYLAHEPLGgATAAIDPAVSEPVLERLAARGWTLTHILNTHHHGDHTGANLDLARRTG 74 579****************99************************************************ PP TIGR03413 69 vkvvgpaee..ripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtLfsaGCGr 135 ++vvg+a++ ripg+t ev+eg+++ l++++v+vlevpGHt+gH+ay+l++++vlFcgDtLfs+GCGr lcl|NCBI__GCF_000009985.1:WP_043747124.1 75 CAVVGAARDseRIPGITLEVSEGETFMLGHAAVTVLEVPGHTSGHVAYWLADSHVLFCGDTLFSLGCGR 143 ******99989********************************************************** PP TIGR03413 136 lfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPs 204 lfegtae+m++sl+kl++Lp +t+ y+aHEYt+ N rFa+ ve +n alk+rl+eve+lra+++pt+P+ lcl|NCBI__GCF_000009985.1:WP_043747124.1 144 LFEGTAEEMWASLKKLRDLPPDTLAYPAHEYTAGNGRFARLVERDNGALKARLDEVERLRAHNRPTVPV 212 ********************************************************************* PP TIGR03413 205 tlaeekatNpFLraeeaevkaalee.ekaeevevfaelRekkdkf 248 +la+e+a NpFLra++a++++a++ ++++ vfaelR++kd f lcl|NCBI__GCF_000009985.1:WP_043747124.1 213 RLADERAANPFLRADTAAIARAVGLePGTDPALVFAELRRRKDVF 257 ***********************9978999*************88 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (257 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.91 // [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