Align 4-hydroxybenzoate 3-monooxygenase (NAD(P)H); 4-hydroxybenzoate 3-hydroxylase; 4HB 3-hydroxylase; EC 1.14.13.33 (characterized)
to candidate HSERO_RS19905 HSERO_RS19905 4-hydroxybenzoate 3-monooxygenase
Query= SwissProt::C4TP09 (394 letters) >FitnessBrowser__HerbieS:HSERO_RS19905 Length = 388 Score = 513 bits (1321), Expect = e-150 Identities = 252/389 (64%), Positives = 306/389 (78%), Gaps = 3/389 (0%) Query: 1 MRTQVGIIGAGPAGLLLSHLLYLQGIESIIIENRTREEIEGTIRAGVLEQGTVDLMNQMG 60 MRTQV IIGAGPAGLLLSHLL+L+GIES+++E R+REEIE TIRAGVLEQGT+D++ + G Sbjct: 1 MRTQVAIIGAGPAGLLLSHLLHLKGIESVVLETRSREEIESTIRAGVLEQGTMDILTETG 60 Query: 61 VGARMMKEGHFHEGFELRFNGRGHRINVHELTGGKYVTVYAQHEVIKDLVAARLQTGGQI 120 VG RM +EG H G EL F GR HRI++ ELTG + +TVYAQHEVIKDLVAARL GQ+ Sbjct: 61 VGERMKREGALHHGIELAFGGRRHRIDLTELTG-QAITVYAQHEVIKDLVAARLAAQGQL 119 Query: 121 HFNVGDVSLHDVDTSSPKIRFRPNKDGELQEIECDFIAGCDGFRGPSRPAIPQSVRKEYQ 180 F+V S+ V+T P++RF +GE +E DFIAGCDGF G SRPAIP S R++YQ Sbjct: 120 LFSVSGTSIEGVETDKPRVRFM--HEGEQHTLEADFIAGCDGFHGVSRPAIPDSKRQDYQ 177 Query: 181 KVYPFSWLGILVEAPPSAHELIYANHERGFALVSTRSPQIQRLYLQVDAQDHIDNWSDDR 240 ++YPF W G+LVEAPPS+ ELIYA HERGF LVSTRSP +QRLY Q D +D +DNWSDDR Sbjct: 178 RIYPFGWFGVLVEAPPSSDELIYAQHERGFVLVSTRSPTVQRLYFQCDPKDSVDNWSDDR 237 Query: 241 IWSELHARLETRDGFKLLEGPIFQKGIVSMRSFVCDPMQHGRLFLAGDAAHIVPPTGAKG 300 IW+E H RLE DG++L EG IFQKGI+ MRSFV PMQHGRLFLAGDAAHIVPPTGAKG Sbjct: 238 IWNEFHTRLENGDGWRLKEGKIFQKGIIGMRSFVSTPMQHGRLFLAGDAAHIVPPTGAKG 297 Query: 301 LNLAAADVQVLARGLEAYYKAGKMEILNRCTEICLRRIWKAERFSWFMTTMLHRDQGHTP 360 LNLA DV+ LA+G++ +Y++ L TE L+RIW+AE FSW+MT+MLH + +P Sbjct: 298 LNLAVGDVKRLAQGIDDFYRSASEAGLASYTEQALKRIWRAEYFSWWMTSMLHTFEDASP 357 Query: 361 FERGIQLAELDYVTSSRAASTSLAENYIG 389 F+R IQ AEL+ V +SRA ST+LAENY+G Sbjct: 358 FQRQIQRAELENVVNSRALSTALAENYVG 386 Lambda K H 0.322 0.139 0.421 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: 465 Number of extensions: 16 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: 394 Length of database: 388 Length adjustment: 31 Effective length of query: 363 Effective length of database: 357 Effective search space: 129591 Effective search space used: 129591 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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