Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate Echvi_2457 Echvi_2457 histidinol-phosphatase
Query= SwissProt::D2QPE6 (382 letters) >FitnessBrowser__Cola:Echvi_2457 Length = 365 Score = 520 bits (1338), Expect = e-152 Identities = 257/382 (67%), Positives = 294/382 (76%), Gaps = 17/382 (4%) Query: 1 MQKIVFIDRDGTLIAEPQPDQQVDSLAKLDFIPKAISAMRKIAEDTTYELVMVTNQDGLG 60 M+K++FIDRDGT+I EP D QVDSL KL+F PKAIS +RKIAE+T YELVMVTNQDGLG Sbjct: 1 MKKVLFIDRDGTIIKEPPVDYQVDSLEKLEFYPKAISNLRKIAEETDYELVMVTNQDGLG 60 Query: 61 TGSFPEDTFWPAHNKMMSTFAGENVNFAAVHIDRHFPHDNSSTRKPGVGMLTQYFEASYD 120 T SFPEDTFWPA KM+ T E V F+A+HID+ F H+N+ TRKP G+LT Y + YD Sbjct: 61 TDSFPEDTFWPAQYKMLKTLEEEGVVFSAIHIDKTFEHENAPTRKPRTGLLTDYLKGDYD 120 Query: 121 LTNSFVIGDRLTDVQLAVNLGAKAILFMPPNGLAAVQSADVSGLTEAMKQAIVLQTGDWD 180 L +SFVIGDR TDVQLA NLG +AI + E + L T WD Sbjct: 121 LAHSFVIGDRKTDVQLAKNLGTQAIF-----------------IGEEAAEGAALSTTSWD 163 Query: 181 EIYEFLRLPARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADL 240 EIYEFLRLP+R V+R+T ETQI + +NLDG G+ + TGL FFDHML+Q+ KH G DL Sbjct: 164 EIYEFLRLPSRIGQVKRSTSETQIEIMVNLDGSGKCQIDTGLPFFDHMLEQLGKHGGTDL 223 Query: 241 AIHVNGDLHIDEHHTIEDTALALGEAYRRALGDKRGISRYGFLLPMDEALAQVGIDFSGR 300 I VNGDLHIDEHHTIEDTALALGEAY +ALGDK+GI RYGFLLPMD+ LAQV IDF GR Sbjct: 224 DIKVNGDLHIDEHHTIEDTALALGEAYLKALGDKKGIYRYGFLLPMDDVLAQVAIDFGGR 283 Query: 301 PWLVWDAEFKREKIGDMPTEMFYHFFKSFSDTALCNLNIKVEGDNEHHKIEAIFKAFAKA 360 PW++W+AEF REKIGDMPTEMFYHFFKSFSDTA CNLNIK EG NEHHKIEAIFK A+A Sbjct: 284 PWMMWEAEFNREKIGDMPTEMFYHFFKSFSDTAKCNLNIKAEGANEHHKIEAIFKGLARA 343 Query: 361 IKMAVRRDINELDNLPSTKGVL 382 IKMAV+RDI L+ LPSTKGVL Sbjct: 344 IKMAVKRDIAALNQLPSTKGVL 365 Lambda K H 0.320 0.136 0.403 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: 472 Number of extensions: 22 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: 382 Length of database: 365 Length adjustment: 30 Effective length of query: 352 Effective length of database: 335 Effective search space: 117920 Effective search space used: 117920 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: 50 (23.9 bits)
Align candidate Echvi_2457 Echvi_2457 (histidinol-phosphatase)
to HMM TIGR01261 (hisB: 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/TIGR01261.hmm # target sequence database: /tmp/gapView.13884.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01261 [M=161] Accession: TIGR01261 Description: hisB_Nterm: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-57 179.0 0.0 3.7e-57 178.4 0.0 1.3 1 lcl|FitnessBrowser__Cola:Echvi_2457 Echvi_2457 histidinol-phosphatas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2457 Echvi_2457 histidinol-phosphatase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.4 0.0 3.7e-57 3.7e-57 1 152 [. 2 153 .. 2 169 .. 0.92 Alignments for each domain: == domain 1 score: 178.4 bits; conditional E-value: 3.7e-57 TIGR01261 1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklk.eagyklvlvtnqdGlGtesfPkedfdkphal 73 +k+lfidrdGt+i+eP+ d+qvd+lekl++ +k+i++l+k+ e++y+lv+vtnqdGlGt+sfP++ f ++ + lcl|FitnessBrowser__Cola:Echvi_2457 2 KKVLFIDRDGTIIKEPPVDYQVDSLEKLEFYPKAISNLRKIAeETDYELVMVTNQDGLGTDSFPEDTFWPAQYK 75 589*************************************962689**************************** PP TIGR01261 74 mlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglkyk 147 ml+ ++ eG+vf+ + i++ f+++n+ +rkP+++ll++yl k ++d ++s+viGdr+td+qla+nlg +++ lcl|FitnessBrowser__Cola:Echvi_2457 76 MLKTLEEEGVVFSAIHIDKTFEHENAPTRKPRTGLLTDYL-KGDYDLAHSFVIGDRKTDVQLAKNLGTQAIFIG 148 ****************************************.678*************************99887 PP TIGR01261 148 eeeln 152 ee + lcl|FitnessBrowser__Cola:Echvi_2457 149 EEAAE 153 77654 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (161 nodes) Target sequences: 1 (365 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.14 // [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