Align hydroxyacylglutathione hydrolase; EC 3.1.2.6 (characterized)
to candidate PfGW456L13_3340 Hydroxyacylglutathione hydrolase (EC 3.1.2.6)
Query= CharProtDB::CH_024825 (251 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3340 Length = 255 Score = 229 bits (585), Expect = 3e-65 Identities = 122/255 (47%), Positives = 156/255 (61%), Gaps = 5/255 (1%) Query: 1 MNLNSIPAFDDNYIWVLNDEAG-RCLIVDPGDAEPVLNAIAAN-NWQPEAIFLTHHHHDH 58 + + ++PAF DNYIW+L D RC +VDPGDA PV +AAN W I +THHHHDH Sbjct: 2 IQITALPAFTDNYIWLLQDHGSKRCAVVDPGDAGPVQAWLAANPGWVLSDILITHHHHDH 61 Query: 59 VGGVKELVEKFPQIVVYGPQETQDKGTTQVVKDGETAFVLGHEFSVIATPGHTLGHICYF 118 VGGV++L +K VYGP +KD + VLG +F V+A PGHTLGHI Y+ Sbjct: 62 VGGVEQL-KKATDAKVYGPASETIPARDVALKDNDKVCVLGWDFDVLAVPGHTLGHIAYY 120 Query: 119 SKPYLFCGDTLFSGGCGRLFEGTASQMYQSLKKLSALPDDTLVCCAHEYTLSNMKFALSI 178 LFCGDTLF+ GCGRLFEGT QMY SL +L+ LP+DTLV C HEYTL N+KFA ++ Sbjct: 121 HHGLLFCGDTLFAAGCGRLFEGTPQQMYSSLTRLAGLPEDTLVYCTHEYTLGNLKFAAAV 180 Query: 179 LPHDLSINDYYRKVKELRAKNQITLPVILKNERQINVFLRTEDIDLINVINEETLLQQ-- 236 P++ + KV R +TLP L E+ N FLR+ + + +E T Sbjct: 181 EPNNPHTAERLAKVTRQRESGIMTLPSTLALEKLTNPFLRSGETSVKEKADERTGTDNSA 240 Query: 237 PEERFAWLRSKKDRF 251 P+ FA LR+ KDRF Sbjct: 241 PDMVFAALRAWKDRF 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: 251 Number of extensions: 11 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
Align candidate PfGW456L13_3340 (Hydroxyacylglutathione hydrolase (EC 3.1.2.6))
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.8294.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-106 339.4 0.0 6.6e-106 339.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3340 Hydroxyacylglutathione hydrolase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3340 Hydroxyacylglutathione hydrolase (EC 3.1.2.6) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 339.2 0.0 6.6e-106 6.6e-106 1 248 [] 4 255 .] 4 255 .] 0.98 Alignments for each domain: == domain 1 score: 339.2 bits; conditional E-value: 6.6e-106 TIGR03413 1 iiaipalsdNyiwllkdeks.eavvvDpgeaepvlealeek.glkleaillTHhH 53 i+a+pa++dNyiwll+d+ s +++vvDpg+a pv+++l+++ g+ l++il+THhH lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3340 4 ITALPAFTDNYIWLLQDHGSkRCAVVDPGDAGPVQAWLAANpGWVLSDILITHHH 58 6799*************9999*****************98769************ PP TIGR03413 54 aDHvggvaellekfpvkvvgpaeeripgltkevkegdevellelevevlevpGHt 108 +DHvggv++l++++++kv+gpa+e+ip+ ++++k++d+v +l+ +++vl+vpGHt lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3340 59 HDHVGGVEQLKKATDAKVYGPASETIPARDVALKDNDKVCVLGWDFDVLAVPGHT 113 ******************************************************* PP TIGR03413 109 lgHiayyleeekvlFcgDtLfsaGCGrlfegtaeqmleslqklaaLpeetkvyca 163 lgHiayy + ++lFcgDtLf+aGCGrlfegt++qm++sl++la Lpe+t+vyc+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3340 114 LGHIAYYHH--GLLFCGDTLFAAGCGRLFEGTPQQMYSSLTRLAGLPEDTLVYCT 166 *********..******************************************** PP TIGR03413 164 HEYtlsNlrFalavepenealkerlkevealrakgkptlPstlaeekatNpFLra 218 HEYtl Nl+Fa+avep+n++ +erl++v+++r++g +tlPstla ek tNpFLr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3340 167 HEYTLGNLKFAAAVEPNNPHTAERLAKVTRQRESGIMTLPSTLALEKLTNPFLRS 221 ******************************************************* PP TIGR03413 219 eeaevkaalee....ekaeevevfaelRekkdkf 248 e++vk++++e +++ + vfa+lR++kd+f lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3340 222 GETSVKEKADErtgtDNSAPDMVFAALRAWKDRF 255 ********99988877888899**********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: 8.72 // [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