Align histidinol-phosphatase (EC 3.1.3.15) (characterized)
to candidate WP_011779146.1 MVAN_RS09600 histidinol-phosphatase
Query= BRENDA::Q8NS80 (260 letters) >NCBI__GCF_000015305.1:WP_011779146.1 Length = 259 Score = 345 bits (885), Expect = e-100 Identities = 171/260 (65%), Positives = 204/260 (78%), Gaps = 4/260 (1%) Query: 1 MSKYADDLALALELAELADSITLDRFEASDLEVSSKPDMTPVSDADLATEEALREKIATA 60 MS DDL LAL LA+ AD++T+ RF A DL V +KPDMTP +DADL E+ LR ++ + Sbjct: 1 MSTLVDDLNLALRLADEADALTMQRFGAVDLRVETKPDMTPATDADLDAEKLLRARLTES 60 Query: 61 RPADSILGEEFGGDVEFSGRQWIIDPIDGTKNYVRGVPVWATLIALLDNGKPVAGVISAP 120 RP DS+ GEEFGG EF+GRQW++DPIDGTKN+VRGVPVW+TLIALL +G PV GVISAP Sbjct: 61 RPQDSVFGEEFGGTREFTGRQWVVDPIDGTKNFVRGVPVWSTLIALLVDGVPVVGVISAP 120 Query: 121 ALARRWWASEGAGAWRTFNGSSPRKLSVSQVSKLDDASLSFSSL-SGWAERDLRDQFVSL 179 AL RRWWA EG GA+ +F G + R++SVS V+ ++ ASLSFS L +GW E+ R +FV L Sbjct: 121 ALGRRWWAGEGQGAFTSFGGDT-RRISVSAVADMEAASLSFSDLATGWEEK--RSRFVEL 177 Query: 180 TDTTWRLRGYGDFFSYCLVAEGAVDIAAEPEVSLWDLAPLSILVTEAGGKFTSLAGVDGP 239 D WR+RGYGDF+SYCLVAEGAVDIA EPEV LWDLAPL ILV EAGG+FT+LAG GP Sbjct: 178 LDAVWRMRGYGDFWSYCLVAEGAVDIAVEPEVKLWDLAPLDILVREAGGRFTNLAGEPGP 237 Query: 240 HGGDAVATNGILHDETLDRL 259 HGG AVATNG+LHD L L Sbjct: 238 HGGSAVATNGLLHDAVLSAL 257 Lambda K H 0.315 0.133 0.396 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: 281 Number of extensions: 16 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: 260 Length of database: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_011779146.1 MVAN_RS09600 (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.1948.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-91 290.9 0.0 4.7e-91 290.7 0.0 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011779146.1 MVAN_RS09600 histidinol-phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011779146.1 MVAN_RS09600 histidinol-phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 290.7 0.0 4.7e-91 4.7e-91 2 251 .. 8 257 .. 7 258 .. 0.97 Alignments for each domain: == domain 1 score: 290.7 bits; conditional E-value: 4.7e-91 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeee 70 l+lal+la+ a++ ++++f+a dl v++k+d+tp t+AD aE+++r+ +++++P+d+++GEEfg ++e lcl|NCBI__GCF_000015305.1:WP_011779146.1 8 LNLALRLADEADALTMQRFGAVDLRVETKPDMTPATDADLDAEKLLRARLTESRPQDSVFGEEFGGTRE 76 67999**************************************************************** PP TIGR02067 71 daeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.ge.rel 137 +++Wv+DPiDGTk+F+rGvPvw+tLiaLl +g pv+Gvis+Palg+r++a +g+ga+++ g+ r++ lcl|NCBI__GCF_000015305.1:WP_011779146.1 77 FTGRQWVVDPIDGTKNFVRGVPVWSTLIALLVDGVPVVGVISAPALGRRWWAGEGQGAFTSFgGDtRRI 145 ***********************************************************9864447*** PP TIGR02067 138 rvsevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyD 206 +vs+va++++A+l++++ a ee+r++f +l ++++++r++gd+++y+lvA+G+vd++ve+e++++D lcl|NCBI__GCF_000015305.1:WP_011779146.1 146 SVSAVADMEAASLSFSDL-ATGWEEKRSRFVELLDAVWRMRGYGDFWSYCLVAEGAVDIAVEPEVKLWD 213 ******************.8999999******************************************* PP TIGR02067 207 iaalipiieeAggvitdwkGkeaeeggeavaaanaalhdevlell 251 +a+l +++ eAgg +t+++G++ +gg+a +a+n lhd+vl +l lcl|NCBI__GCF_000015305.1:WP_011779146.1 214 LAPLDILVREAGGRFTNLAGEPGPHGGSA-VATNGLLHDAVLSAL 257 *****************************.99**********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (259 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: 6.50 // [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