Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate RR42_RS03715 RR42_RS03715 inositol monophosphatase
Query= reanno::Phaeo:GFF2154 (250 letters) >FitnessBrowser__Cup4G11:RR42_RS03715 Length = 263 Score = 228 bits (580), Expect = 1e-64 Identities = 127/251 (50%), Positives = 156/251 (62%), Gaps = 6/251 (2%) Query: 1 MADAARQAILPYFRSAGLQSDNKLDEGFDPVTIADRAAEQAMRSVLSELRPEDSILGEEF 60 +A AA A LPYFRSA D K FDPVT AD+AAE+AMR ++ PE ILGEE Sbjct: 18 LAQAAGNASLPYFRSAPAVED-KGGRHFDPVTAADKAAERAMRDLILAKYPEHGILGEEE 76 Query: 61 GETHGQSGRTWVLDPIDGTRGFISGTPTWGVLIALGDADGPFLGIVDQPYIGERFIGTPE 120 G S TWVLDPIDGTR FI+G P WG LIAL D P +GI+DQP+ ERF G Sbjct: 77 DRVAGTSPLTWVLDPIDGTRAFITGLPLWGTLIALNDGQRPVIGIMDQPFTRERFSGDGS 136 Query: 121 GASLTGPLGHSALVTRATDSLSEATLFTTFPEVGTEAER-AAFQRVSAQVRLTRYGMDCY 179 A L G L TR L++A L T PE+ +A + AAF+RV+ R+ RYG DCY Sbjct: 137 RAWLNG----QPLRTRPCADLAQAKLMCTTPEMFEDAAQFAAFRRVADAARMQRYGGDCY 192 Query: 180 AYALLAAGQCDLVIEAGLNAYDIQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATAELH 239 AY ++AAG D V+EAGL AYD+QA I ++Q AGGV+T+W G A +GG V+A LH Sbjct: 193 AYCMVAAGHVDAVVEAGLKAYDVQALIPIVQGAGGVMTSWTGGDAQQGGTVVACGDPRLH 252 Query: 240 AAALALIQQTA 250 +AL+ A Sbjct: 253 QQIIALLNAPA 263 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: 212 Number of extensions: 6 Number of successful extensions: 3 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: 263 Length adjustment: 24 Effective length of query: 226 Effective length of database: 239 Effective search space: 54014 Effective search space used: 54014 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 RR42_RS03715 RR42_RS03715 (inositol monophosphatase)
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.15435.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-99 316.5 0.0 7.2e-99 316.3 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS03715 RR42_RS03715 inositol monophosph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS03715 RR42_RS03715 inositol monophosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 316.3 0.0 7.2e-99 7.2e-99 3 252 .] 13 260 .. 11 260 .. 0.97 Alignments for each domain: == domain 1 score: 316.3 bits; conditional E-value: 7.2e-99 TIGR02067 3 alalelaeaageailkyfrasdlkvdkksdk.tpVteADraaEeaireliaakfPddgilGEEfgeeee 70 +a+ la+aag+a l+yfr ++dk ++ +pVt AD+aaE+a+r+li ak+P++gilGEE + ++ lcl|FitnessBrowser__Cup4G11:RR42_RS03715 13 DFAAGLAQAAGNASLPYFRSAPAVEDKGGRHfDPVTAADKAAERAMRDLILAKYPEHGILGEEEDRVAG 81 68999***************999999999989************************************* PP TIGR02067 71 daeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallnggerelrv 139 ++ +WvlDPiDGT++Fi+G+P+wgtLiaL+++++pv+G+++qP+++erf ++ g++a+lng ++lr+ lcl|FitnessBrowser__Cup4G11:RR42_RS03715 82 TSPLTWVLDPIDGTRAFITGLPLWGTLIALNDGQRPVIGIMDQPFTRERFSGD-GSRAWLNG--QPLRT 147 **************************************************997.56667776..8**** PP TIGR02067 140 sevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDia 208 + +a+l++A l++t+p+++ed ++ +af++++++ar++ryggdcyay++vA+G+vd vvea+l++yD++ lcl|FitnessBrowser__Cup4G11:RR42_RS03715 148 RPCADLAQAKLMCTTPEMFEDAAQFAAFRRVADAARMQRYGGDCYAYCMVAAGHVDAVVEAGLKAYDVQ 216 ********************************************************************* PP TIGR02067 209 alipiieeAggvitdwkGkeaeeggeavaaanaalhdevlellk 252 alipi+++Aggv+t+w+G +a++gg++va+++++lh+++++ll+ lcl|FitnessBrowser__Cup4G11:RR42_RS03715 217 ALIPIVQGAGGVMTSWTGGDAQQGGTVVACGDPRLHQQIIALLN 260 ****************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (252 nodes) Target sequences: 1 (263 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: 10.68 // [ok]
This GapMind analysis is from Apr 09 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