Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate Echvi_2441 Echvi_2441 Methylmalonyl-CoA mutase, N-terminal domain/subunit
Query= BRENDA::Q8F222 (1125 letters) >FitnessBrowser__Cola:Echvi_2441 Length = 1125 Score = 1498 bits (3877), Expect = 0.0 Identities = 754/1125 (67%), Positives = 901/1125 (80%), Gaps = 12/1125 (1%) Query: 6 YTPKHKVRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQEDAQG 65 Y PK VR +TAASLFDGHDA+INIMRRI+QS G EVIHLGHNRSV+EIV CAIQED Q Sbjct: 8 YKPKSHVRIVTAASLFDGHDAAINIMRRIIQSVGCEVIHLGHNRSVQEIVSCAIQEDVQA 67 Query: 66 IAITSYQGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRIYSPDD 125 IAITSYQGGH+E+FKYM DLL+EKGAGHIK+FGGGGGTILP+EIKEL +YGV RIY+PDD Sbjct: 68 IAITSYQGGHIEFFKYMYDLLQEKGAGHIKIFGGGGGTILPAEIKELHAYGVARIYAPDD 127 Query: 126 GRELGLQGMINDLIRRSDFIPPITFNGTLHSSLKD-KNPLAIAQMITLVENTFEREDLEK 184 GR +GLQGMINDL+ ++DF +G +L D ++P IA+ I+ EN + Sbjct: 128 GRSMGLQGMINDLVGQADFPLGDKLDG---GALPDVRHPERIARWISAAENFPDAYQ--- 181 Query: 185 STLNEKLNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDPSKRK 244 ++ EK K+VPVLGITGTGGAGKSSL DEL RRFL+DFP+K +AI+SVDPSKRK Sbjct: 182 -SMREKQGHGGEDKTVPVLGITGTGGAGKSSLVDELARRFLVDFPDKHLAIISVDPSKRK 240 Query: 245 TGGALLGDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVETAGI 304 TGGALLGDRIRMN+I H RVYMRS ATR+AN++L+K+VK +++++K AGFDL+I+ET+GI Sbjct: 241 TGGALLGDRIRMNAIHHPRVYMRSLATRQANLSLSKHVKDAVDIVKMAGFDLVILETSGI 300 Query: 305 GQSDSEITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRDVKKQ 364 GQSD+E+ + AD++LYVMTPEYGAA+QLEKIDM+D+ADLIA+NKFDK+GA DALRDVKKQ Sbjct: 301 GQSDTEVADHADLSLYVMTPEYGAASQLEKIDMLDFADLIALNKFDKKGAFDALRDVKKQ 360 Query: 365 FQRSRQLFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLDWSSSYEKEEGAS 424 F R+ L+D + +PV GTIASQFNDPG N LY ++ L+ D++ S Sbjct: 361 FVRNHGLWDAKDEELPVIGTIASQFNDPGMNRLYRELMLRLTALKIADFTPSDGASLEEL 420 Query: 425 EKIFIIPPDRVRYLAEIREECGRYDQFTKNESDKARKLFQLSGAIEVLKSSGQDISI--- 481 EK+FIIPP R RYLAEI EE RY+Q+ + + A +L+ + AIE + + S Sbjct: 421 EKLFIIPPSRTRYLAEIVEENQRYEQWAATQKELANRLYGVKKAIETFEEEAEGESAVME 480 Query: 482 -LKLEYSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVSNTTVSLSNLKIP 540 L+ Y+ + N L E + L +W+E + +Y + FT+ VR KEI + + SLS +IP Sbjct: 481 SLEAAYTALTNKLDAENLQWLENWKELVGSYANDQFTFMVRGKEIAIQTFSTSLSGTRIP 540 Query: 541 KVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAGEGGPERTNARFH 600 KVA+PK++ WG++++W F+EN PG+FPFT+GVFPFKR GEDPTRMFAGEGGPERTN RFH Sbjct: 541 KVALPKYEAWGDLLQWKFKENVPGKFPFTAGVFPFKREGEDPTRMFAGEGGPERTNRRFH 600 Query: 601 YVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDAKKLYSGFDLCNP 660 YVS MPA+RLSTAFDSVTLYGEDPG RPDIYGKIGNSGV+I LDD KKLY+GFDL +P Sbjct: 601 YVSKDMPAKRLSTAFDSVTLYGEDPGYRPDIYGKIGNSGVNICCLDDMKKLYAGFDLADP 660 Query: 661 TTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIEKSVRQKIESIYKEKKFPIPKYN 720 TSVSMTINGPA + AFFMNTAIDQ CE++I G E V K++ +Y+E P+Y Sbjct: 661 RTSVSMTINGPAATMTAFFMNTAIDQQCERYIYDKGSEGEVEAKLDEMYRENGLERPRYQ 720 Query: 721 TQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADILKEDQAQNTCIFS 780 +PEGN+GLGL+LLGVTGD+VL KEVYE IK +TL VRGTVQADILKEDQAQNTCIFS Sbjct: 721 GTVPEGNNGLGLLLLGVTGDQVLPKEVYESIKADTLTKVRGTVQADILKEDQAQNTCIFS 780 Query: 781 TEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFTLANGLTYVEYFLS 840 TEF+L++MGD+QE+FI VRNFYSVSISGYHIAEAGANPITQ+A TL+NG TYVEY++S Sbjct: 781 TEFSLRLMGDVQEYFIDQGVRNFYSVSISGYHIAEAGANPITQLALTLSNGFTYVEYYVS 840 Query: 841 RGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGANDRSAMLKYHIQTSG 900 RGM ++ FAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMK KYGAN+RS MLKYHIQTSG Sbjct: 841 RGMDVNAFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKLKYGANERSQMLKYHIQTSG 900 Query: 901 RSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRAMAIQLIINRE 960 RSLHAQEI FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTE SVRRAMAIQLIIN+E Sbjct: 901 RSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEASVRRAMAIQLIINKE 960 Query: 961 LGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMMYQRNKIQEESLYY 1020 LGL+KNENP QG+FIIEELTDLVE+A+ EF +I+ERGGVLGAME MYQR KIQEESL+Y Sbjct: 961 LGLAKNENPLQGAFIIEELTDLVEEAVYAEFERITERGGVLGAMETMYQRGKIQEESLHY 1020 Query: 1021 ESLKHNGEFPVIGVNTFLSKEGSPTIVPQEVIRSTDEEKQAQISALREFHKRNEKDIENR 1080 E+LKH G +P+IGVNTFLS GSPTI P EVIR+T EEK+ QI L H++ E Sbjct: 1021 ETLKHAGTYPIIGVNTFLSSAGSPTITPGEVIRATQEEKEMQIKGLENLHRKYEFQSVEL 1080 Query: 1081 LRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125 L LK +++N N+F +LME K SLGQ+THALYEVGGQ+RR+M Sbjct: 1081 LNDLKEAAVTNENLFSQLMEAVKCCSLGQITHALYEVGGQFRRNM 1125 Lambda K H 0.317 0.135 0.379 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: 3229 Number of extensions: 144 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: 1125 Length of database: 1125 Length adjustment: 46 Effective length of query: 1079 Effective length of database: 1079 Effective search space: 1164241 Effective search space used: 1164241 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 (21.6 bits) S2: 58 (26.9 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