Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate 349731 BT0203 histidine biosynthesis bifunctional protein hisB (NCBI ptt file)
Query= SwissProt::Q8ABA7 (374 letters) >FitnessBrowser__Btheta:349731 Length = 374 Score = 765 bits (1975), Expect = 0.0 Identities = 374/374 (100%), Positives = 374/374 (100%) Query: 1 MKKKILFIDRDGTLVIEPPIDYQLDSLEKLEFYPRVFRNLGFIRSKLDFEFVMVTNQDGL 60 MKKKILFIDRDGTLVIEPPIDYQLDSLEKLEFYPRVFRNLGFIRSKLDFEFVMVTNQDGL Sbjct: 1 MKKKILFIDRDGTLVIEPPIDYQLDSLEKLEFYPRVFRNLGFIRSKLDFEFVMVTNQDGL 60 Query: 61 GTSSFPEDTFWPAHNLMLKTLAGEGITFDDILIDRSFPEDNAPTRKPRTGMLTKYIDNPE 120 GTSSFPEDTFWPAHNLMLKTLAGEGITFDDILIDRSFPEDNAPTRKPRTGMLTKYIDNPE Sbjct: 61 GTSSFPEDTFWPAHNLMLKTLAGEGITFDDILIDRSFPEDNAPTRKPRTGMLTKYIDNPE 120 Query: 121 YDLAESFVIGDRPTDVELAKNLGCRAIYLQEATDDLKEKGLEEVCALATTDWDQVAEFLF 180 YDLAESFVIGDRPTDVELAKNLGCRAIYLQEATDDLKEKGLEEVCALATTDWDQVAEFLF Sbjct: 121 YDLAESFVIGDRPTDVELAKNLGCRAIYLQEATDDLKEKGLEEVCALATTDWDQVAEFLF 180 Query: 181 AGERKAEVRRTTKETDIYVSLNLDGNGGCDISTGLGFFDHMLEQIGKHSGMDLTIRVKGD 240 AGERKAEVRRTTKETDIYVSLNLDGNGGCDISTGLGFFDHMLEQIGKHSGMDLTIRVKGD Sbjct: 181 AGERKAEVRRTTKETDIYVSLNLDGNGGCDISTGLGFFDHMLEQIGKHSGMDLTIRVKGD 240 Query: 241 LEVDEHHTIEDTAIALGECIYQALGSKRGIERYGYALPMDDCLCQVCLDFGGRPWLVWDA 300 LEVDEHHTIEDTAIALGECIYQALGSKRGIERYGYALPMDDCLCQVCLDFGGRPWLVWDA Sbjct: 241 LEVDEHHTIEDTAIALGECIYQALGSKRGIERYGYALPMDDCLCQVCLDFGGRPWLVWDA 300 Query: 301 EFNREKIGEMPTEMFLHFFKSLSDAAKMNLNIKAEGQNEHHKIEGIFKALARALKMALKR 360 EFNREKIGEMPTEMFLHFFKSLSDAAKMNLNIKAEGQNEHHKIEGIFKALARALKMALKR Sbjct: 301 EFNREKIGEMPTEMFLHFFKSLSDAAKMNLNIKAEGQNEHHKIEGIFKALARALKMALKR 360 Query: 361 DIYHFELPSSKGVL 374 DIYHFELPSSKGVL Sbjct: 361 DIYHFELPSSKGVL 374 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: 604 Number of extensions: 13 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: 374 Length of database: 374 Length adjustment: 30 Effective length of query: 344 Effective length of database: 344 Effective search space: 118336 Effective search space used: 118336 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 349731 BT0203 (histidine biosynthesis bifunctional protein hisB (NCBI ptt file))
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.31318.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-59 184.5 0.0 7.7e-59 183.9 0.0 1.3 1 lcl|FitnessBrowser__Btheta:349731 BT0203 histidine biosynthesis bi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:349731 BT0203 histidine biosynthesis bifunctional protein hisB (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 183.9 0.0 7.7e-59 7.7e-59 1 149 [. 3 152 .. 3 163 .. 0.96 Alignments for each domain: == domain 1 score: 183.9 bits; conditional E-value: 7.7e-59 TIGR01261 1 qkilfidrdGtlieePksdfqvdaleklklekkvipallklk.eagyklvlvtnqdGlGtesfPkedfdkphalml 75 +kilfidrdGtl+ eP+ d+q+d+lekl++ + v +l ++ ++++++v+vtnqdGlGt+sfP++ f +h+lml lcl|FitnessBrowser__Btheta:349731 3 KKILFIDRDGTLVIEPPIDYQLDSLEKLEFYPRVFRNLGFIRsKLDFEFVMVTNQDGLGTSSFPEDTFWPAHNLML 78 59************************************8876378******************************* PP TIGR01261 76 qifkseGivfddvlicphfledncacrkPkiklleeylkkekidkersyviGdretdlqlaenlgirglkykee 149 + + eGi+fdd+li+++f+edn+ +rkP++++l++y+ + ++d ++s+viGdr+td++la+nlg r++ ++e lcl|FitnessBrowser__Btheta:349731 79 KTLAGEGITFDDILIDRSFPEDNAPTRKPRTGMLTKYIDNPEYDLAESFVIGDRPTDVELAKNLGCRAIYLQEA 152 ********************************************************************988865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (161 nodes) Target sequences: 1 (374 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: 11.32 // [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