Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate WP_043526145.1 JH15_RS00990 hydroxyacylglutathione hydrolase
Query= CharProtDB::CH_024825 (251 letters) >NCBI__GCF_000759345.1:WP_043526145.1 Length = 255 Score = 213 bits (541), Expect = 4e-60 Identities = 111/250 (44%), Positives = 151/250 (60%), Gaps = 5/250 (2%) Query: 6 IPAFDDNYIWVLN-DEAGRCLIVDPGDAEPVLNAIAANNWQPEAIFLTHHHHDHVGGVKE 64 IPA DNYIW+L D + +VDPGDA PV+ + I +THHHHDH GG++ Sbjct: 7 IPALSDNYIWLLRQDTSNEVAVVDPGDARPVIELLEREGLTLGTILITHHHHDHTGGLEA 66 Query: 65 LVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYFSK---P 121 L+ ++ V+ GPQ G + + +G+ VLG F V+ PGHTL HI +F+ P Sbjct: 67 LIRQYRPRVI-GPQNPDIVGIDERLAEGDECHVLGRRFEVLEMPGHTLDHIAFFAAGIPP 125 Query: 122 YLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSILPH 181 L GD LFSGGCGRLFEGT QM+ SL KL+ALPD+TL+ AHEYTL+N++FA + P Sbjct: 126 LLLAGDALFSGGCGRLFEGTPEQMHASLAKLAALPDETLIFAAHEYTLANLRFAKAADPD 185 Query: 182 DLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLLQQPEERF 241 + +I Y + + +R +++ TLP L ERQ+N FLRTE + N + + F Sbjct: 186 NPAIGAYLEECQRVRDQDKPTLPTQLARERQVNPFLRTEQPGVRNAASAQGDTTTSLATF 245 Query: 242 AWLRSKKDRF 251 LR+ KDRF Sbjct: 246 TTLRAWKDRF 255 Lambda K H 0.321 0.138 0.425 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: 219 Number of extensions: 13 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: 251 Length of database: 255 Length adjustment: 24 Effective length of query: 227 Effective length of database: 231 Effective search space: 52437 Effective search space used: 52437 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 WP_043526145.1 JH15_RS00990 (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.3744514.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-102 326.9 0.0 4.2e-102 326.8 0.0 1.0 1 NCBI__GCF_000759345.1:WP_043526145.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000759345.1:WP_043526145.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 326.8 0.0 4.2e-102 4.2e-102 2 248 .] 5 255 .] 4 255 .] 0.98 Alignments for each domain: == domain 1 score: 326.8 bits; conditional E-value: 4.2e-102 TIGR03413 2 iaipalsdNyiwllkdeks.eavvvDpgeaepvlealeekglkleaillTHhHaDHvggvaellekfpvkvvg 73 +ipalsdNyiwll++++s e++vvDpg+a+pv+e le++gl+l +il+THhH+DH+gg ++l+++++ +v+g NCBI__GCF_000759345.1:WP_043526145.1 5 LPIPALSDNYIWLLRQDTSnEVAVVDPGDARPVIELLEREGLTLGTILITHHHHDHTGGLEALIRQYRPRVIG 77 689************99999***************************************************** PP TIGR03413 74 paeeripgltkevkegdevellelevevlevpGHtlgHiayyleee.kvlFcgDtLfsaGCGrlfegtaeqml 145 p++ +i g++++++egde+++l++++evle+pGHtl+Hia++++ ++l +gD+Lfs GCGrlfegt+eqm+ NCBI__GCF_000759345.1:WP_043526145.1 78 PQNPDIVGIDERLAEGDECHVLGRRFEVLEMPGHTLDHIAFFAAGIpPLLLAGDALFSGGCGRLFEGTPEQMH 150 ******************************************9977799************************ PP TIGR03413 146 eslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLra 218 +sl klaaLp+et++++aHEYtl+NlrFa+a++p+n+a+ ++l+e+++ r+++kptlP++la+e+++NpFLr+ NCBI__GCF_000759345.1:WP_043526145.1 151 ASLAKLAALPDETLIFAAHEYTLANLRFAKAADPDNPAIGAYLEECQRVRDQDKPTLPTQLARERQVNPFLRT 223 ************************************************************************* PP TIGR03413 219 eeaevkaalee..ekaeevevfaelRekkdkf 248 e++ v++a+++ ++++++++f++lR++kd+f NCBI__GCF_000759345.1:WP_043526145.1 224 EQPGVRNAASAqgDTTTSLATFTTLRAWKDRF 255 ******99999777889999**********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (255 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: 14.32 // [ok]
This GapMind analysis is from Sep 24 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