Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_038217853.1 Q392_RS29640 histidinol-phosphatase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >NCBI__GCF_000745855.1:WP_038217853.1 Length = 258 Score = 244 bits (624), Expect = 1e-69 Identities = 128/255 (50%), Positives = 164/255 (64%), Gaps = 2/255 (0%) Query: 4 PCPTPLVTLAERLADASGPVIRQYFRTPVAVDDKADASPVTIADREAERTIRAIIEAERP 63 P PL+ A LADA+ YFR P+ + KAD SPVT+ADR AE+ +R ++ A+ P Sbjct: 3 PAIHPLLATAHALADAAARQSMAYFRQPLEIVTKADDSPVTLADRAAEQAMRDVLAAQAP 62 Query: 64 DDGIYGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIV 123 +DGIYGEE G + LDA VWV+DPIDGT+SFITG P++GTLIA GR LG+ID P++ Sbjct: 63 EDGIYGEEHGQQRLDAGRVWVLDPIDGTRSFITGSPLWGTLIAAFSGGRVELGMIDMPVL 122 Query: 124 RDRWLGVEGRPTLFNGQPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVSV 183 +RW+G +G + NGQP RVR C LA A + TTSPD+F AD F ++ + Sbjct: 123 GERWIGQDG-VAMRNGQPVRVRGCT-RLAEARIVTTSPDIFAPADWAVFDALSRRCAMRR 180 Query: 184 YGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSGRVV 243 +GGDCY Y LA G DLVVE+GL+ YD+ V+ AGG++TDW+GRPL RVV Sbjct: 181 FGGDCYGYAQLAGGTIDLVVETGLQPYDYLGPAGVIEAAGGVITDWEGRPLGLQPDCRVV 240 Query: 244 AAGDARTHRETLAAL 258 AA HR LA L Sbjct: 241 AAATPELHRAALAVL 255 Lambda K H 0.320 0.139 0.424 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: 280 Number of extensions: 13 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: 260 Length of database: 258 Length adjustment: 24 Effective length of query: 236 Effective length of database: 234 Effective search space: 55224 Effective search space used: 55224 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_038217853.1 Q392_RS29640 (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.4004837.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-88 281.2 0.1 4.4e-88 281.0 0.1 1.0 1 NCBI__GCF_000745855.1:WP_038217853.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038217853.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 281.0 0.1 4.4e-88 4.4e-88 2 252 .] 9 256 .. 8 256 .. 0.96 Alignments for each domain: == domain 1 score: 281.0 bits; conditional E-value: 4.4e-88 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeeedaey 74 la a++la+aa+++ + yfr+ ++v k +d+ pVt ADraaE+a+r+++aa+ P+dgi+GEE+g+++ da++ NCBI__GCF_000745855.1:WP_038217853.1 9 LATAHALADAAARQSMAYFRQPLEIVTKADDS-PVTLADRAAEQAMRDVLAAQAPEDGIYGEEHGQQRLDAGR 80 57899****************88887776666.**************************************** PP TIGR02067 75 vWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallnggerelrvsevaklsd 147 vWvlDPiDGT+sFi+G P+wgtLia ++g++ lG+i++P+lger++++ g ++ +++rv+ +++l++ NCBI__GCF_000745855.1:WP_038217853.1 81 VWVLDPIDGTRSFITGSPLWGTLIAAFSGGRVELGMIDMPVLGERWIGQDGVAMRNG---QPVRVRGCTRLAE 150 ************************************************999887664...7************ PP TIGR02067 148 AvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaalipiieeAggv 220 A +vttsp +++++++ + f++l r++ + r+ggdcy+ya +A G++dlvve++l+pyD+ + +ie Aggv NCBI__GCF_000745855.1:WP_038217853.1 151 ARIVTTSP-DIFAPADWAVFDALSRRCAMRRFGGDCYGYAQLAGGTIDLVVETGLQPYDYLGPAGVIEAAGGV 222 ********.799************************************************************* PP TIGR02067 221 itdwkGkeae..eggeavaaanaalhdevlellk 252 itdw+G+++ + ++vaaa+++lh+++l++l+ NCBI__GCF_000745855.1:WP_038217853.1 223 ITDWEGRPLGlqPDCRVVAAATPELHRAALAVLQ 256 ********9776899***************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (258 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: 19.07 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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