Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_012041664.1 BBTA_RS06555 histidinol-phosphatase
Query= reanno::azobra:AZOBR_RS03845 (260 letters) >NCBI__GCF_000015165.1:WP_012041664.1 Length = 261 Score = 243 bits (621), Expect = 2e-69 Identities = 132/251 (52%), Positives = 166/251 (66%), Gaps = 9/251 (3%) Query: 15 RLADASGPVIRQYFRTPVAVDDKA---DASPVTIADREAERTIRAIIEAERPDDGIYGEE 71 RLA ASG I +FRT ++VD+K+ D PVT ADR AE +R +I+A P GI GEE Sbjct: 12 RLATASGETILPFFRTSLSVDNKSSRHDFDPVTEADRAAEAVMRRLIKANFPQHGIVGEE 71 Query: 72 FGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRDRWLGVE 131 FG + DA++VWV+DPIDGTKSFI G PI+GTLIALLH+G PV G++ QP + +R+ G Sbjct: 72 FGNEREDADYVWVLDPIDGTKSFIAGFPIWGTLIALLHKGIPVFGMMHQPFIGERFAGDN 131 Query: 132 GRPTLFNGQPAR---VRECAGGLAAATLGTTSPDLFPGADQDAFRRVAGAAKVSVYGGDC 188 G N R VR C L A TTSP L AD+ AF R ++S YGGDC Sbjct: 132 GSANYRNAAGERRLSVRRCE-RLQDAVCYTTSPLLMNDADRAAFARAESEVRLSRYGGDC 190 Query: 189 YSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSGRVVAAGDA 248 YSY +LAAG+ DLV+E+ LK YD AAL+P++ GAGG++TDWDG P A + GR++AAGD Sbjct: 191 YSYCMLAAGHLDLVIETELKPYDIAALIPIINGAGGIVTDWDGGP--AQNGGRIIAAGDK 248 Query: 249 RTHRETLAALA 259 R H L LA Sbjct: 249 RVHEAALKRLA 259 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: 229 Number of extensions: 8 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: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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_012041664.1 BBTA_RS06555 (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.16590.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-107 344.4 0.0 2.2e-107 344.2 0.0 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012041664.1 BBTA_RS06555 histidinol-phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015165.1:WP_012041664.1 BBTA_RS06555 histidinol-phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 344.2 0.0 2.2e-107 2.2e-107 2 251 .. 7 258 .. 6 259 .. 0.97 Alignments for each domain: == domain 1 score: 344.2 bits; conditional E-value: 2.2e-107 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdk..tpVteADraaEeaireliaakfPddgilGEEfgee 68 +a++ +la+a+ge+il++fr+s ++++k+s++ +pVteADraaE+++r+li+a+fP++gi+GEEfg+e lcl|NCBI__GCF_000015165.1:WP_012041664.1 7 SAFIGRLATASGETILPFFRTSLSVDNKSSRHdfDPVTEADRAAEAVMRRLIKANFPQHGIVGEEFGNE 75 68999****************8888888887789*********************************** PP TIGR02067 69 eedaeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.gere 136 +eda+yvWvlDPiDGTksFi+G+P+wgtLiaLl+kg pv+G+++qP++gerf +++g+++++n ger+ lcl|NCBI__GCF_000015165.1:WP_012041664.1 76 REDADYVWVLDPIDGTKSFIAGFPIWGTLIALLHKGIPVFGMMHQPFIGERFAGDNGSANYRNAaGERR 144 ***************************************************************9777** PP TIGR02067 137 lrvsevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspy 205 l+v+++ +l+dAv +ttsp l++ ++r+af++ ++++rl+ryggdcy+y+++A+G+ dlv+e+el+py lcl|NCBI__GCF_000015165.1:WP_012041664.1 145 LSVRRCERLQDAVCYTTSP-LLMNDADRAAFARAESEVRLSRYGGDCYSYCMLAAGHLDLVIETELKPY 212 *******************.89999******************************************** PP TIGR02067 206 DiaalipiieeAggvitdwkGkeaeeggeavaaanaalhdevlell 251 Diaalipii++Agg++tdw+G +a++gg+++aa+++++h+++l++l lcl|NCBI__GCF_000015165.1:WP_012041664.1 213 DIAALIPIINGAGGIVTDWDGGPAQNGGRIIAAGDKRVHEAALKRL 258 *******************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (261 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: 8.78 // [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