Align hydroxyacylglutathione hydrolase (EC 3.1.2.6) (characterized)
to candidate AO353_23490 AO353_23490 hydroxyacylglutathione hydrolase
Query= BRENDA::Q8ZRM2 (251 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23490 Length = 255 Score = 236 bits (602), Expect = 3e-67 Identities = 119/255 (46%), Positives = 167/255 (65%), Gaps = 5/255 (1%) Query: 1 MNLNSIPAFQDNYIWVLTNDEG-RCVIVDPGEAAPVLKAIAEHK-WMPEAIFLTHHHHDH 58 + ++++PAF DNYIW+L + RC +VDPG+AAPV +A H W I +THHHHDH Sbjct: 2 IQISALPAFTDNYIWLLQDHRSQRCAVVDPGDAAPVQAWLAMHPGWQLSDILVTHHHHDH 61 Query: 59 VGGVKELLQHFPQMTVYGPAETQDKGATHLVGDGDTIRVLGEKFTLFATPGHTLGHVCYF 118 VGGV++L + TVYGPA G + D D + VLG +F ++A PGHTLGH+ Y+ Sbjct: 62 VGGVEQL-KKATGATVYGPASENIPGRDIALNDNDRVSVLGREFDVYAVPGHTLGHIAYY 120 Query: 119 SRPYLFCGDTLFSGGCGRLFEGTPSQMYQSLMKINSLPDDTLICCAHEYTLANIKFALSI 178 + LFCGDTLF+ GCGRLFEGTP+QM+ SL ++ +LP+DTL+ C HEYTL+N++FA ++ Sbjct: 121 HQGLLFCGDTLFAAGCGRLFEGTPAQMHHSLSRLAALPEDTLVYCTHEYTLSNLRFAAAV 180 Query: 179 LPHDSFINEYYRKVKELRVKKQMTLPVILKNERKINLFLRTEDIDLINEINKET--ILQQ 236 P++ I E KV +LR M+LP L E+ N FLRT + + ++++ + Sbjct: 181 EPNNPDIAERLEKVSQLRESGGMSLPSTLALEKLTNPFLRTGETSVKEKVDERNGQDNRA 240 Query: 237 PEARFAWLRSKKDTF 251 P FA LR+ KDTF Sbjct: 241 PSEVFAALRAWKDTF 255 Lambda K H 0.323 0.140 0.436 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: 248 Number of extensions: 9 Number of successful extensions: 3 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 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 bits)
Align candidate AO353_23490 AO353_23490 (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.31077.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-109 351.5 0.0 1.3e-109 351.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_23490 AO353_23490 hydroxyacylglutathio Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_23490 AO353_23490 hydroxyacylglutathione hydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 351.3 0.0 1.3e-109 1.3e-109 1 248 [] 4 255 .] 4 255 .] 0.98 Alignments for each domain: == domain 1 score: 351.3 bits; conditional E-value: 1.3e-109 TIGR03413 1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeek.glkleaillTHhHaDHvggvael 63 i a+pa++dNyiwll+d++s +++vvDpg+a+pv+++l+ + g++l++il+THhH+DHvggv++l lcl|FitnessBrowser__pseudo3_N2E3:AO353_23490 4 ISALPAFTDNYIWLLQDHRSqRCAVVDPGDAAPVQAWLAMHpGWQLSDILVTHHHHDHVGGVEQL 68 5789**************999*****************98769********************** PP TIGR03413 64 lekfpvkvvgpaeeripgltkevkegdevellelevevlevpGHtlgHiayyleeekvlFcgDtL 128 +++++++v+gpa+e+ipg + +++++d+v++l++e++v++vpGHtlgHiayy + ++lFcgDtL lcl|FitnessBrowser__pseudo3_N2E3:AO353_23490 69 KKATGATVYGPASENIPGRDIALNDNDRVSVLGREFDVYAVPGHTLGHIAYYHQ--GLLFCGDTL 131 ******************************************************..********* PP TIGR03413 129 fsaGCGrlfegtaeqmleslqklaaLpeetkvycaHEYtlsNlrFalavepenealkerlkevea 193 f+aGCGrlfegt++qm++sl++laaLpe+t+vyc+HEYtlsNlrFa+avep+n++++erl++v++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_23490 132 FAAGCGRLFEGTPAQMHHSLSRLAALPEDTLVYCTHEYTLSNLRFAAAVEPNNPDIAERLEKVSQ 196 ***************************************************************** PP TIGR03413 194 lrakgkptlPstlaeekatNpFLraeeaevkaalee....ekaeevevfaelRekkdkf 248 lr++g ++lPstla ek tNpFLr+ e++vk++++e +++ + evfa+lR++kd+f lcl|FitnessBrowser__pseudo3_N2E3:AO353_23490 197 LRESGGMSLPSTLALEKLTNPFLRTGETSVKEKVDErngqDNRAPSEVFAALRAWKDTF 255 **********************************998887788999***********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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.37 // [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