Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate YP_001328382.1 Smed_2717 histidinol-phosphate phosphatase
Query= reanno::Phaeo:GFF2154 (250 letters) >NCBI__GCF_000017145.1:YP_001328382.1 Length = 288 Score = 235 bits (600), Expect = 6e-67 Identities = 121/247 (48%), Positives = 159/247 (64%), Gaps = 1/247 (0%) Query: 1 MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF 60 +ADAA+ +P FR G NKL+ GFDPVT ADR+AE ++R+++ P+ ILGEE Sbjct: 41 LADAAKAETMPRFR-VGTSVLNKLEGGFDPVTEADRSAEASIRALIESSFPDHGILGEEH 99 Query: 61 GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE 120 G WV+DPIDGTR FISG P WG LI L +G++DQP+ GER+ E Sbjct: 100 GNIGLDRELVWVIDPIDGTRAFISGLPVWGTLIGLYRNGKAIMGLMDQPFTGERYFADGE 159 Query: 121 GASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAERAAFQRVSAQVRLTRYGMDCYA 180 A GP G L TR +LS+A LFTT P + A + F+ + A+VRL RYG DCYA Sbjct: 160 KALYRGPDGERVLATRPCHALSDAVLFTTSPHLYQGALKERFETLQAKVRLFRYGCDCYA 219 Query: 181 YALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELHA 240 +ALLAAG DLVIE GL YD+ I +I+ AGG++TNWQG PA GG+++AA + E+HA Sbjct: 220 FALLAAGHVDLVIECGLKPYDVGGLIPLIEQAGGIITNWQGGPAEMGGEIIAAGSREVHA 279 Query: 241 AALALIQ 247 AL +++ Sbjct: 280 RALEVLK 286 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: 230 Number of extensions: 9 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: 288 Length adjustment: 25 Effective length of query: 225 Effective length of database: 263 Effective search space: 59175 Effective search space used: 59175 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_001328382.1 Smed_2717 (histidinol-phosphate 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.1082.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-100 321.7 0.0 1.8e-100 321.5 0.0 1.0 1 lcl|NCBI__GCF_000017145.1:YP_001328382.1 Smed_2717 histidinol-phosphate p Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017145.1:YP_001328382.1 Smed_2717 histidinol-phosphate phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 321.5 0.0 1.8e-100 1.8e-100 2 252 .] 35 286 .. 34 286 .. 0.98 Alignments for each domain: == domain 1 score: 321.5 bits; conditional E-value: 1.8e-100 TIGR02067 2 lalalelaeaageailkyfrasdlkvdkksdk.tpVteADraaEeaireliaakfPddgilGEEfgeee 69 ++++++la+aa+++++++fr +++ +k + +pVteADr+aE+ ir+li+++fPd+gilGEE+g++ lcl|NCBI__GCF_000017145.1:YP_001328382.1 35 RSFFDRLADAAKAETMPRFRVGTSVLNKLEGGfDPVTEADRSAEASIRALIESSFPDHGILGEEHGNIG 103 67999***********************99999************************************ PP TIGR02067 70 edaeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallng.gerel 137 d+e vWv+DPiDGT++Fi+G+PvwgtLi+L+++gk+++G+++qP++ger++a+ +++ ++ + ger l lcl|NCBI__GCF_000017145.1:YP_001328382.1 104 LDRELVWVIDPIDGTRAFISGLPVWGTLIGLYRNGKAIMGLMDQPFTGERYFADGEKALYRGPdGERVL 172 *************************************************************98667*** PP TIGR02067 138 rvsevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyD 206 +++ +++lsdAvl+ttsp +l + + +e+fe l++k+rl ryg+dcya+al+A+G+vdlv+e++l+pyD lcl|NCBI__GCF_000017145.1:YP_001328382.1 173 ATRPCHALSDAVLFTTSP-HLYQGALKERFETLQAKVRLFRYGCDCYAFALLAAGHVDLVIECGLKPYD 240 ******************.9************************************************* PP TIGR02067 207 iaalipiieeAggvitdwkGkeaeeggeavaaanaalhdevlellk 252 + lip+ie+Agg+it+w+G +ae+gge++aa+++++h+++le+lk lcl|NCBI__GCF_000017145.1:YP_001328382.1 241 VGGLIPLIEQAGGIITNWQGGPAEMGGEIIAAGSREVHARALEVLK 286 *******************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (288 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.43 // [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