Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_036263646.1 DL86_RS16490 histidinol-phosphatase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >NCBI__GCF_000746085.1:WP_036263646.1 Length = 265 Score = 227 bits (578), Expect = 2e-64 Identities = 124/259 (47%), Positives = 161/259 (62%), Gaps = 16/259 (6%) Query: 14 ERLADASGPVIRQYFRTPVAVDDKADAS---PVTIADREAERTIRAIIEAERPDDGIYGE 70 E+LAD +G +I +FRT + +DK PVT AD AE +R +IE P GI GE Sbjct: 11 EKLADIAGDMILPFFRTALGAEDKNVGGMFDPVTEADHAAEAAMRRLIEQTFPHHGIIGE 70 Query: 71 EFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRDRWLGV 130 EFG+ DAE+VWV+DPIDGTKSFI G PI+G+LI LLH G P G++ QP R+R++G Sbjct: 71 EFGSVRSDAEYVWVLDPIDGTKSFIAGMPIWGSLIGLLHNGAPTYGMMVQPFTRERFIG- 129 Query: 131 EGRPTLFNG---------QPARVRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKV 181 +G ++ G + R C+ L+ ATL TTSP L+ AFRRV ++ Sbjct: 130 DGAGAVWRGPGLNHAIVERKLATRICS-NLSKATLMTTSPLLYSDTKLAAFRRVEAKTRL 188 Query: 182 SVYGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSGR 241 S YGGDCY++ +LAAG+ D V+ESGLK YD A L P++ GAGG++TDWDG AT G Sbjct: 189 SRYGGDCYAFAMLAAGHVDCVIESGLKTYDIAPLTPIIEGAGGIVTDWDG--ASATGGGD 246 Query: 242 VVAAGDARTHRETLAALAG 260 +VA G R H E L L G Sbjct: 247 IVACGSPRIHDEVLKLLRG 265 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: 243 Number of extensions: 12 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: 260 Length of database: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 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_036263646.1 DL86_RS16490 (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.21800.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-99 316.9 0.0 5.4e-99 316.7 0.0 1.0 1 lcl|NCBI__GCF_000746085.1:WP_036263646.1 DL86_RS16490 histidinol-phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000746085.1:WP_036263646.1 DL86_RS16490 histidinol-phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 316.7 0.0 5.4e-99 5.4e-99 2 251 .. 7 263 .. 6 264 .. 0.97 Alignments for each domain: == domain 1 score: 316.7 bits; conditional E-value: 5.4e-99 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdk..tpVteADraaEeaireliaakfPddgilGEEfgee 68 +a++++la++ag++il++fr+ ++dk+ +pVteAD+aaE+a+r+li+++fP++gi+GEEfg+ lcl|NCBI__GCF_000746085.1:WP_036263646.1 7 AAFVEKLADIAGDMILPFFRTALGAEDKNVGGmfDPVTEADHAAEAAMRRLIEQTFPHHGIIGEEFGSV 75 6899*****************9999999888889*********************************** PP TIGR02067 69 eedaeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallngge... 134 ++daeyvWvlDPiDGTksFi+G+P+wg Li+Ll++g+p+ G++ qP+++erf+++ +++++ +g lcl|NCBI__GCF_000746085.1:WP_036263646.1 76 RSDAEYVWVLDPIDGTKSFIAGMPIWGSLIGLLHNGAPTYGMMVQPFTRERFIGDGAGAVWRGPGLnha 144 *******************************************************99999998743468 PP TIGR02067 135 ...relrvsevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvvea 200 r+l+++ +++ls+A+l+ttsp l + ++ +af+++++k+rl+ryggdcya+a++A+G+vd v+e+ lcl|NCBI__GCF_000746085.1:WP_036263646.1 145 iveRKLATRICSNLSKATLMTTSP-LLYSDTKLAAFRRVEAKTRLSRYGGDCYAFAMLAAGHVDCVIES 212 999*********************.8999999************************************* PP TIGR02067 201 elspyDiaalipiieeAggvitdwkGkeaeeggeavaaanaalhdevlell 251 +l++yDia+l+piie+Agg++tdw+G +a+ gg++va++++++hdevl+ll lcl|NCBI__GCF_000746085.1:WP_036263646.1 213 GLKTYDIAPLTPIIEGAGGIVTDWDGASATGGGDIVACGSPRIHDEVLKLL 263 ************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (265 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: 9.72 // [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