Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate YP_002827372.1 NGR_c28730 inositol mono-phosphatase family protein
Query= reanno::Phaeo:GFF2154 (250 letters) >NCBI__GCF_000018545.1:YP_002827372.1 Length = 258 Score = 243 bits (621), Expect = 2e-69 Identities = 126/247 (51%), Positives = 164/247 (66%), Gaps = 1/247 (0%) Query: 1 MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF 60 +ADAA+ LP FR+ G NKL+ GFDPVT AD++AE A+R ++ + PE ILGEE Sbjct: 11 LADAAKAETLPRFRT-GTSVVNKLEGGFDPVTEADQSAEAAIRRLIEDSFPEHGILGEEH 69 Query: 61 GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE 120 G WV+DPIDGTR FISG P WG LI L +G++DQP+ GER+ + Sbjct: 70 GNIGLDREHVWVIDPIDGTRAFISGLPVWGTLIGLYRNGKAIMGLMDQPFTGERYFADGQ 129 Query: 121 GASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCYA 180 + GP G + L TRA D+LS+A LFTT P + T +A F+ + A+VRL RYG DCYA Sbjct: 130 KSIYRGPGGENVLSTRACDALSDAVLFTTSPHLYTGELKARFEALQAKVRLFRYGCDCYA 189 Query: 181 YALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELHA 240 +ALLAAG DLV+E GL YD+ I +I+ AGGVVT+WQG PA GG+V+AA + ELHA Sbjct: 190 FALLAAGHVDLVVECGLKPYDVGGLIPLIEQAGGVVTDWQGGPAEMGGEVIAAGSPELHA 249 Query: 241 AALALIQ 247 AL +++ Sbjct: 250 QALQMLR 256 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: 222 Number of extensions: 8 Number of successful extensions: 1 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: 258 Length adjustment: 24 Effective length of query: 226 Effective length of database: 234 Effective search space: 52884 Effective search space used: 52884 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 YP_002827372.1 NGR_c28730 (inositol mono-phosphatase family protein)
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.26741.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-102 326.8 0.0 5.3e-102 326.6 0.0 1.0 1 lcl|NCBI__GCF_000018545.1:YP_002827372.1 NGR_c28730 inositol mono-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000018545.1:YP_002827372.1 NGR_c28730 inositol mono-phosphatase family protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 326.6 0.0 5.3e-102 5.3e-102 2 251 .. 5 255 .. 4 256 .. 0.98 Alignments for each domain: == domain 1 score: 326.6 bits; conditional E-value: 5.3e-102 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdk.tpVteADraaEeaireliaakfPddgilGEEfgeee 69 ++++++la+aa++++l++fr+ +++v+k + +pVteAD++aE+air+li+++fP++gilGEE+g++ lcl|NCBI__GCF_000018545.1:YP_002827372.1 5 RSFFDRLADAAKAETLPRFRTGTSVVNKLEGGfDPVTEADQSAEAAIRRLIEDSFPEHGILGEEHGNIG 73 67999************************9999************************************ PP TIGR02067 70 edaeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.gerel 137 d+e+vWv+DPiDGT++Fi+G+PvwgtLi+L+++gk+++G+++qP++ger++a+ ++ ++ + ge+ l lcl|NCBI__GCF_000018545.1:YP_002827372.1 74 LDREHVWVIDPIDGTRAFISGLPVWGTLIGLYRNGKAIMGLMDQPFTGERYFADGQKSIYRGPgGENVL 142 **********************************************************9999867799* PP TIGR02067 138 rvsevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyD 206 +++++ +lsdAvl+ttsp +l + e +++fe+l++k+rl ryg+dcya+al+A+G+vdlvve++l+pyD lcl|NCBI__GCF_000018545.1:YP_002827372.1 143 STRACDALSDAVLFTTSP-HLYTGELKARFEALQAKVRLFRYGCDCYAFALLAAGHVDLVVECGLKPYD 210 ******************.9************************************************* PP TIGR02067 207 iaalipiieeAggvitdwkGkeaeeggeavaaanaalhdevlell 251 + lip+ie+Aggv+tdw+G +ae+gge++aa++++lh+++l++l lcl|NCBI__GCF_000018545.1:YP_002827372.1 211 VGGLIPLIEQAGGVVTDWQGGPAEMGGEVIAAGSPELHAQALQML 255 *******************************************98 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.33 // [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