Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_010527280.1 GQW_RS0106955 bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::Q8ABA7 (374 letters) >NCBI__GCF_000220155.1:WP_010527280.1 Length = 378 Score = 526 bits (1355), Expect = e-154 Identities = 256/375 (68%), Positives = 303/375 (80%), Gaps = 4/375 (1%) Query: 3 KKILFIDRDGTLVIEPPIDYQLDSLEKLEFYPRVFRNLGFIRSKLDFEFVMVTNQDGLGT 62 K+ILFIDRDGT++ EPPIDYQ+DSLEKLEFYP V NL I LDF+ VMVTNQDGLGT Sbjct: 5 KRILFIDRDGTIIKEPPIDYQVDSLEKLEFYPGVMVNLARIVRHLDFQLVMVTNQDGLGT 64 Query: 63 SSFPEDTFWPAHNLMLKTLAGEGITFDDILIDRSFPEDNAPTRKPRTGMLTKYIDNPEYD 122 SFPE+TFWPAHN ML+TL GEGI F I IDRSFPEDNAPTRKPRTGML Y+ YD Sbjct: 65 PSFPEETFWPAHNKMLETLKGEGIQFSAIHIDRSFPEDNAPTRKPRTGMLKDYLSG-NYD 123 Query: 123 LAESFVIGDRPTDVELAKNLGCRAIYL---QEATDDLKEKGLEEVCALATTDWDQVAEFL 179 L SFVIGDR TDVELAKN+GC+AI + +EA L+E+ L+ C L +T W+++A++L Sbjct: 124 LDNSFVIGDRLTDVELAKNMGCKAILMKKPEEAIPLLEEQNLKNYCVLCSTRWEEIADYL 183 Query: 180 FAGERKAEVRRTTKETDIYVSLNLDGNGGCDISTGLGFFDHMLEQIGKHSGMDLTIRVKG 239 F ER+ V R T ET I V+LNLDG G CDISTGLGFFDHMLEQIG+HSG DL I+V G Sbjct: 184 FTKERQVTVERNTSETKIKVTLNLDGTGSCDISTGLGFFDHMLEQIGRHSGCDLQIKVTG 243 Query: 240 DLEVDEHHTIEDTAIALGECIYQALGSKRGIERYGYALPMDDCLCQVCLDFGGRPWLVWD 299 DL VDEHHTIEDTA+ALGE + +ALG KRGIERYG++LPMDDC+ V +DFGGRPWLVW Sbjct: 244 DLHVDEHHTIEDTALALGEALKKALGDKRGIERYGFSLPMDDCMAHVAIDFGGRPWLVWK 303 Query: 300 AEFNREKIGEMPTEMFLHFFKSLSDAAKMNLNIKAEGQNEHHKIEGIFKALARALKMALK 359 A+F REK+G++PTEMF HFFKSL+DAA N+ IKA+G+NEHHKIE IFKALARA+K A++ Sbjct: 304 AKFKREKVGDLPTEMFYHFFKSLADAAAANIYIKAKGKNEHHKIEAIFKALARAIKAAIR 363 Query: 360 RDIYHFELPSSKGVL 374 +D + +LPS+KG L Sbjct: 364 KDPLNRQLPSTKGFL 378 Lambda K H 0.321 0.140 0.422 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: 463 Number of extensions: 23 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: 374 Length of database: 378 Length adjustment: 30 Effective length of query: 344 Effective length of database: 348 Effective search space: 119712 Effective search space used: 119712 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 WP_010527280.1 GQW_RS0106955 (bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB)
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.3558987.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.1e-58 181.0 0.0 9.3e-58 180.4 0.0 1.3 1 NCBI__GCF_000220155.1:WP_010527280.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000220155.1:WP_010527280.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.4 0.0 9.3e-58 9.3e-58 2 150 .. 6 154 .. 5 165 .. 0.95 Alignments for each domain: == domain 1 score: 180.4 bits; conditional E-value: 9.3e-58 TIGR01261 2 kilfidrdGtlieePksdfqvdaleklklekkvipallkl.keagyklvlvtnqdGlGtesfPkedfdkphal 73 +ilfidrdGt+i+eP+ d+qvd+lekl++ ++v+ +l ++ ++++++lv+vtnqdGlGt+sfP+e f +h++ NCBI__GCF_000220155.1:WP_010527280.1 6 RILFIDRDGTIIKEPPIDYQVDSLEKLEFYPGVMVNLARIvRHLDFQLVMVTNQDGLGTPSFPEETFWPAHNK 78 79***********************************9973679***************************** PP TIGR01261 74 mlqifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglky 146 ml+ +k eGi+f+ + i+++f+edn+ +rkP++++l++yl + ++d ++s+viGdr td++la+n+g +++ + NCBI__GCF_000220155.1:WP_010527280.1 79 MLETLKGEGIQFSAIHIDRSFPEDNAPTRKPRTGMLKDYL-SGNYDLDNSFVIGDRLTDVELAKNMGCKAILM 150 ****************************************.778**************************998 PP TIGR01261 147 keee 150 k++e NCBI__GCF_000220155.1:WP_010527280.1 151 KKPE 154 8766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (161 nodes) Target sequences: 1 (378 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: 22.06 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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