Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate H281DRAFT_02676 H281DRAFT_02676 xanthine dehydrogenase, molybdenum binding subunit apoprotein (EC 1.17.1.4)
Query= SwissProt::O33819 (769 letters) >FitnessBrowser__Burk376:H281DRAFT_02676 Length = 788 Score = 309 bits (792), Expect = 3e-88 Identities = 235/789 (29%), Positives = 375/789 (47%), Gaps = 49/789 (6%) Query: 11 VGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIA 70 +G R + + + G+ Y D+ P+ L +LRS HAHA+I++ID +AA L+GV A Sbjct: 16 IGKRVTRTEDKKLLQGQGSYVDDVHLPNMLQAAVLRSSHAHAKIVSIDCTAARELKGVHA 75 Query: 71 VCTGAE----------TPVPFGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEKAL 120 V T A+ + +P + + LA +V + G+ VA V A + AE A Sbjct: 76 VYTHADLSGRARGRAPSMLPNPAIRFERTQELLASTEVTFAGEAVAFVVADNRYIAEDAC 135 Query: 121 ALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAAAFAEADLIREKT 180 LI+V+Y+ LPA + ++ + H D +N++ + FGD+ AAF A + E+T Sbjct: 136 GLIEVEYDTLPAVADCRDGLRPESPLCHTDAKDNVVAHIEMGFGDIDAAFNGAPHVVEET 195 Query: 181 YTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPF 240 Y + ME LAE+ LT+ ++ Q P++ + L+ D+ ++RV+ Sbjct: 196 YWQNRGSAHPMETRGYLAEFHAANGELTVWSSGQAPHHEKKNLVELLEWDAEKLRVLMND 255 Query: 241 LGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIA---HRGRPWTEVKMKIGLK 297 +GGGFG + E + + A K V+ ++ R E F+A R + WT +KI L+ Sbjct: 256 VGGGFGPKLPFYPEEALVAIAAVALKRPVKWIEDRREHFLAVTQERDQWWT---VKIALE 312 Query: 298 KDGKIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAM 357 DGKI + LE GA+ +GIIT + G Y IPA+ VYTN + Sbjct: 313 NDGKIRGVKLEMVHDNGAFLPWGIITPYISITTTPGPYVIPAMGAKLDVVYTNKCATSPV 372 Query: 358 RGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINML--PQIPYVTMYAQ------RVMSY 409 RG G A E +L + LG+D ++R N++ Q+PY + R S Sbjct: 373 RGAGRPQAVFAMERILDKAARALGMDRAELRWRNLIQPEQMPYDAGFIYRDGSPLRYDSG 432 Query: 410 GVPEC----LEKVKAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLK 465 P C LE+ K +S + + +GR +GI ++ FV GT P ++ Sbjct: 433 DYPACQKAALERAKYSSFAQRKAEARREGRFIGIGMASFVEGTGM------GPFEGATVR 486 Query: 466 LDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRV 525 + +G I ++TGA+ GQG T +Q+ AE L V L I VI+ D+ G+++SRV Sbjct: 487 VQANGRIAVITGASPQGQGHKTTFAQICAEQLNVPLETIDVITGDTGGISMGVGTFASRV 546 Query: 526 TFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAA 585 T GN+ AA+ + ++ A + E++ +++ + +S+ ++ K + Sbjct: 547 TVNAGNSVYIAAQAVGEKMLTLTAHLWKCKPEELLLVEGHVARRAGIEQRMSYGQLAKIS 606 Query: 586 MVDSGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVW 645 G +T P + A +C VVE VD TG +T Sbjct: 607 QGMPG-------FTMPEGLTAGLEETKYFSPAQSTYCNGTAVVELEVDRETGHITILNYV 659 Query: 646 VAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYD-NGRMVHGNILDYRVPTIVESPD 704 +A D GK +NP+ V+GQ G V G+G A E YD N + + N +Y +P + P+ Sbjct: 660 MAHDSGKLINPMIVDGQVIGSVAHGIGNATLEWMQYDENAQPITTNFGEYLLPMATDVPN 719 Query: 705 IEVIIVESMDPNGPFGAKEASEG----MLAGFLPAIHEAVYEAVGVRATDFPLSPDRITE 760 I+++ +E+ P P G K A EG A + AI +A+ E GV T+ PL P R+ + Sbjct: 720 IDIVHLETPSPLNPLGVKGAGEGGTIPAAAAIVAAIEDALSE-YGVEFTEAPLVPQRVFQ 778 Query: 761 LLDAKEAAA 769 L KEA A Sbjct: 779 KL--KEAGA 785 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: 1346 Number of extensions: 74 Number of successful extensions: 9 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: 788 Length adjustment: 41 Effective length of query: 728 Effective length of database: 747 Effective search space: 543816 Effective search space used: 543816 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