Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate SM_b20132 SM_b20132 dehydrogenase
Query= SwissProt::O33819 (769 letters) >FitnessBrowser__Smeli:SM_b20132 Length = 772 Score = 399 bits (1025), Expect = e-115 Identities = 260/773 (33%), Positives = 415/773 (53%), Gaps = 43/773 (5%) Query: 11 VGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIA 70 VG D +EKVTG A+Y D+A P L ++ RS AHARI +IDTS A AL+GV A Sbjct: 19 VGKSVKRSDTLEKVTGTARYAGDVALPGMLHAKMKRSNIAHARIRSIDTSKALALKGVKA 78 Query: 71 VCTGAETPVPFGV-------LPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEKALALI 123 V T + P + +++Y L D+VRY G+ VAAVAA+ E AE+A+ALI Sbjct: 79 VLTHEDVPRVLHAGSPHPRSASVTKDQYILD-DRVRYWGEGVAAVAAVSEEIAERAVALI 137 Query: 124 KVDYEVLPAYMTPKAAMKAGAIALHDD--KPNNILREVHAEFGDVAAAFAEADLIREKTY 181 +V+YE LP T +AA GA +H++ N +L V GDV FAEADLI E+ Y Sbjct: 138 EVEYEPLPGLFTIEAASVPGAPPIHENGLDRNQVLPPVFVTRGDVDRGFAEADLILEREY 197 Query: 182 TFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPFL 241 +ME N ++++D LT+ T+TQ + V +A L + ++RVI + Sbjct: 198 DLGRPTPAYMEPNVCVSQWDG-NGKLTMWTSTQSAFMVRGTLAEVLGVPLNKVRVIVDHM 256 Query: 242 GGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIGLKKDGK 301 GGGFGA+ + E + LLAR+ V++ +R+ETF+ R R ++ +K G KDG+ Sbjct: 257 GGGFGAKQDLFQNEFLCALLARQTGRPVKMEFSRKETFLGGRSRHPGKIWLKQGFTKDGR 316 Query: 302 IAALALEATQAGGAYAGYGI-ITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGH 360 I A T GAY +G +T + T AL LY ++ + +YTN+P GA RG+ Sbjct: 317 IVAREARVTFNSGAYGSHGPGVTNVGTAALT-SLYRCENVRLEGRCIYTNSPIAGAFRGY 375 Query: 361 GTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECLEKVKA 420 G V T A + ++ E E+LG D + + +N + + + ++ +G+ +C+ +V Sbjct: 376 GVVQTYYALDLMMDEAAEKLGFDPAEFKLMNAVREGD-IAPSGHPIVGHGLGDCIRRVME 434 Query: 421 ASGWEE----RKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLT 476 + W E K + K RG+GI + G+S + +A V K++ DG +TL+T Sbjct: 435 ETNWHELRRREKPETVKRRGIGIGCE--MHGSSAYPGIKEQGNAIV--KMNEDGTVTLIT 490 Query: 477 GAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGNASISA 536 G A +G G++T SQ+ AE LGV + V+ D+ + P D G+++S T++ G A+ A Sbjct: 491 GTAGLGTGAHTALSQIVAEELGVPFEAVSVVQGDTDIVPWDIGAFASHTTYLGGRAAQLA 550 Query: 537 AEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAAM-VDSGTITVK 595 A +++ +++ AA L A E++ + D +V+ + + E V + + + Sbjct: 551 AADVRRQVLEHAAPMLKAEPENLAIRDGFVVVTNGSNRSIRLSEAVGPQRGMPAVQLVGV 610 Query: 596 GTYTCPTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVWVAVDVGKALN 655 GTY T + +AA E VD TG+V +V ++G+ ++ Sbjct: 611 GTYM-----------------PTKSYSFAAHFAEVEVDTETGEVAVLQVVPVHEIGRVIH 653 Query: 656 PLAVEGQTQGGVWMGMGQALSEETVYD--NGRMVHGNILDYRVPTIVESPDIEVIIVESM 713 P+A GQ +GG+ G+G LSE+ V D +GR ++ + +DY++P ++ P I II+E+ Sbjct: 654 PIAAAGQIEGGIQQGIGHTLSEDYVIDLTDGRSLNPSFVDYKMPLSMDMPSIRTIILETA 713 Query: 714 -DPNGPFGAKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDAK 765 DP GP+GAK E + PAI A+Y+A+GVR +P++P+++ L +K Sbjct: 714 PDPGGPYGAKGVGEDPIIAIGPAIANAIYDAIGVRFHHYPITPEQVLNALKSK 766 Lambda K H 0.317 0.134 0.386 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: 1266 Number of extensions: 64 Number of successful extensions: 11 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: 769 Length of database: 772 Length adjustment: 41 Effective length of query: 728 Effective length of database: 731 Effective search space: 532168 Effective search space used: 532168 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: 55 (25.8 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