Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate CA265_RS22275 CA265_RS22275 urocanate hydratase
Query= reanno::SB2B:6937476 (670 letters) >FitnessBrowser__Pedo557:CA265_RS22275 Length = 668 Score = 996 bits (2574), Expect = 0.0 Identities = 483/666 (72%), Positives = 551/666 (82%), Gaps = 1/666 (0%) Query: 5 MTFAEQIKQGIPAELPSPKPYPADANRAPKRKDILTAAEKQLAVRNALRYFPAEWHQELA 64 M F Q+ GIP+ LP+ KP + + AP RKD+LTA EK+LAV+NALRYFP WHQELA Sbjct: 1 MDFKAQLLAGIPSTLPAKKPRNTELSHAPVRKDVLTADEKKLAVKNALRYFPKAWHQELA 60 Query: 65 AEFAKELNDFGRIYMYRFKPEYAMKARAISEYPAKCEQAAAIMLMVDNNLDPAVAQHPEE 124 EF EL ++G IYMYRF P+YA+ AR I+ YP AAAIMLM+ NNLDPA+AQHPEE Sbjct: 61 QEFLTELENYGHIYMYRFMPDYAIYARDIAAYPCLTVHAAAIMLMIQNNLDPAIAQHPEE 120 Query: 125 LITYGGNGAVFQNWAQYRLTMKYLSEMEADQTLHLYSGHPMGLFPSSVDAPRVVVTNGMM 184 LITYGGNG+VFQNWAQY LTM+YL+ M QTL++YSGHP GLFPS+ APRVVVTNGMM Sbjct: 121 LITYGGNGSVFQNWAQYLLTMQYLATMTDQQTLNIYSGHPQGLFPSNTAAPRVVVTNGMM 180 Query: 185 IPNYSKPDDWERFNALGVTQYGQMTAGSFMYIGPQGIVHGTTITVMNGFRKVLEKGDSPK 244 +PNYS P+D E+FNALGVTQYGQMTAGS+MYIGPQGIVHGT IT+MN FRK G Sbjct: 181 VPNYSSPEDLEKFNALGVTQYGQMTAGSYMYIGPQGIVHGTAITLMNAFRKKGFYGKDTA 240 Query: 245 GKIFLTAGLGGMSGAQPKAGNIAGCITVCAEVNPKAATKRHAQGWVDELIDNMDALVARV 304 GKIFLTAGLGGMSGAQ KAGNI GCITVCAEVNPKAATKR QGWVDELIDN+D L+ RV Sbjct: 241 GKIFLTAGLGGMSGAQTKAGNIVGCITVCAEVNPKAATKRQQQGWVDELIDNLDELINRV 300 Query: 305 KQAQANEEVVSIAFIGNVVNVWEAFDEHDIFVHLGSDQTSLHNPWSGGYYPVDISYDESN 364 AQ +E VS+A+IGN+V+VWE FD+ +I V +GSDQTSLHNP+SGGYYPV +S+ E+N Sbjct: 301 IVAQKEKETVSLAYIGNIVDVWERFDQENIEVAIGSDQTSLHNPYSGGYYPVGLSFAEAN 360 Query: 365 RLIREEPELFKTKVQATLKRHADAINRHTAKGTYFFDYGNAFLLEASRAGGDVMAENGID 424 ++ P FK VQ +LKR A +IN+HT KGTYFFDYGNAFLLE SRAG DVM+ NGID Sbjct: 361 EMMAGAPGQFKVYVQDSLKRQAASINKHTGKGTYFFDYGNAFLLECSRAGADVMSPNGID 420 Query: 425 FKYPSYVQDILGPMCFDYGFGPFRWVCTSGNSADLDRTDAIAAEVLARIMAEAPAEIQQQ 484 FKYPSYV+DILGP+CFDYGFGPFRWVC SGN DLD TD +A EV+ I APAEIQQQ Sbjct: 421 FKYPSYVEDILGPLCFDYGFGPFRWVCASGNENDLDLTDQMAKEVMEEIKLSAPAEIQQQ 480 Query: 485 MQDNITWIKDAKQNKLVVGSQARILYADAEGRMEIAKAFNDAISRGEI-GPVVLGRDHHD 543 +QDNI WI AK+NKLVVGS+ARILYADAEGR +IA FN AI GE+ PV+LGRDHHD Sbjct: 481 LQDNINWISAAKENKLVVGSKARILYADAEGRAKIALRFNQAIKTGELSAPVILGRDHHD 540 Query: 544 VSGTDSPFRETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGM 603 VSGTDSPFRETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGM Sbjct: 541 VSGTDSPFRETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGM 600 Query: 604 LLDGTEAAERRLKSMLLFDVNNGIARRSWARNEEANFAIKREMARTPKLKVTLANSVDDD 663 +LDGTE A +L++ML +DVNNGIARRSWARN+EA FAI+REM RT LK+TL N VDD+ Sbjct: 601 VLDGTEQAAEKLQNMLFYDVNNGIARRSWARNKEARFAIEREMERTGTLKITLPNLVDDE 660 Query: 664 IINGLE 669 +++GLE Sbjct: 661 VLDGLE 666 Lambda K H 0.318 0.134 0.404 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: 1284 Number of extensions: 46 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: 670 Length of database: 668 Length adjustment: 39 Effective length of query: 631 Effective length of database: 629 Effective search space: 396899 Effective search space used: 396899 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: 54 (25.4 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