Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_066921539.1 ACG33_RS12155 histidinol-phosphatase
Query= reanno::Phaeo:GFF2154 (250 letters) >NCBI__GCF_001579945.1:WP_066921539.1 Length = 281 Score = 212 bits (540), Expect = 6e-60 Identities = 115/244 (47%), Positives = 150/244 (61%), Gaps = 1/244 (0%) Query: 1 MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF 60 +AD A ILP+FR+ L +NK +GFDPVT+ADR AE A+R + P ILGEE Sbjct: 31 LADLAGAQILPHFRTRLLDVENKDRQGFDPVTLADREAEAAIRREIQRTYPTHGILGEEH 90 Query: 61 GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE 120 G G S TWV+DPIDGTR F+ G WG LIAL D P LG++ QPY GE F+G+ + Sbjct: 91 GLQVGASPYTWVIDPIDGTRAFVLGQLHWGTLIALNDGTRPVLGVMRQPYTGETFLGSEQ 150 Query: 121 GASLTGPLGHSALVTRATDSLSEATLFTTFPEV-GTEAERAAFQRVSAQVRLTRYGMDCY 179 GA L + L RA L EA L T P + R AF+RV+A+ R R+G DCY Sbjct: 151 GAQLRRGSQTTRLSARAGVRLEEAVLCATDPLMFAAPGLRPAFERVAARARAVRFGGDCY 210 Query: 180 AYALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELH 239 L+AAG DLV+EA L +D+QA I +I+ AGG++T+W G+ A E +V+ A+ A LH Sbjct: 211 TPCLVAAGSSDLVVEADLKPWDVQALIPIIEGAGGIITDWAGQAAWEADKVVIASGAGLH 270 Query: 240 AAAL 243 A + Sbjct: 271 AQVI 274 Lambda K H 0.317 0.134 0.392 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: 224 Number of extensions: 11 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: 250 Length of database: 281 Length adjustment: 25 Effective length of query: 225 Effective length of database: 256 Effective search space: 57600 Effective search space used: 57600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_066921539.1 ACG33_RS12155 (histidinol-phosphatase)
to HMM TIGR02067 (hisN: histidinol-phosphatase (EC 3.1.3.15))
# 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.aa/TIGR02067.hmm # target sequence database: /tmp/gapView.5565.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02067 [M=252] Accession: TIGR02067 Description: his_9_HisN: histidinol-phosphatase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-88 282.5 0.0 1.7e-88 282.3 0.0 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066921539.1 ACG33_RS12155 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066921539.1 ACG33_RS12155 histidinol-phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 282.3 0.0 1.7e-88 1.7e-88 2 252 .] 25 278 .. 24 278 .. 0.98 Alignments for each domain: == domain 1 score: 282.3 bits; conditional E-value: 1.7e-88 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdk..tpVteADraaEeaireliaakfPddgilGEEfgee 68 l++a +la++ag++il++fr++ l v++k+++ +pVt ADr+aE+air+ i++++P +gilGEE+g + lcl|NCBI__GCF_001579945.1:WP_066921539.1 25 LEFAVHLADLAGAQILPHFRTRLLDVENKDRQgfDPVTLADREAEAAIRREIQRTYPTHGILGEEHGLQ 93 6899*************************9999************************************ PP TIGR02067 69 eedaeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallngge.re 136 +++ y+Wv+DPiDGT++F+ G wgtLiaL+++ +pvlGv++qP++ge f+++++++ l++g++ + lcl|NCBI__GCF_001579945.1:WP_066921539.1 94 VGASPYTWVIDPIDGTRAFVLGQLHWGTLIALNDGTRPVLGVMRQPYTGETFLGSEQGAQLRRGSQtTR 162 ********************************************************99999998556** PP TIGR02067 137 lrvsevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspy 205 l++++ +l++Avl+ t+p ++++++ r afe+++++ar +r+ggdcy +lvA+G+ dlvvea+l+p+ lcl|NCBI__GCF_001579945.1:WP_066921539.1 163 LSARAGVRLEEAVLCATDPLMFAAPGLRPAFERVAARARAVRFGGDCYTPCLVAAGSSDLVVEADLKPW 231 ********************************************************************* PP TIGR02067 206 DiaalipiieeAggvitdwkGkeaeeggeavaaanaalhdevlellk 252 D++alipiie+Agg+itdw+G+ a e ++v+a+ a lh++v+e+l+ lcl|NCBI__GCF_001579945.1:WP_066921539.1 232 DVQALIPIIEGAGGIITDWAGQAAWEADKVVIASGAGLHAQVIEALN 278 ********************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (281 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: 00:00:00.01 # Mc/sec: 6.66 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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