Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate N515DRAFT_0973 N515DRAFT_0973 methylmalonyl-CoA mutase
Query= BRENDA::Q8F222 (1125 letters) >FitnessBrowser__Dyella79:N515DRAFT_0973 Length = 1155 Score = 1302 bits (3369), Expect = 0.0 Identities = 675/1139 (59%), Positives = 850/1139 (74%), Gaps = 28/1139 (2%) Query: 12 VRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQEDAQGIAITSY 71 +RF+TAASLFDGHDA+INIMRRI+QS G EVIHLGHNRSV ++V A+QEDA IA++SY Sbjct: 20 LRFVTAASLFDGHDAAINIMRRIIQSQGAEVIHLGHNRSVEDVVRAALQEDADAIALSSY 79 Query: 72 QGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRIYSPDDGRELGL 131 QGGHVEYFKYM+D+LKE GA HI+VFGGGGGTI P EI+EL++YGV RIY P+DG +LGL Sbjct: 80 QGGHVEYFKYMVDMLKEHGAAHIRVFGGGGGTITPEEIRELQAYGVERIYHPNDGMKLGL 139 Query: 132 QGMINDLIRRSDFIPPITFNGTLHSSLKDKNPLAIAQMITLVENTFEREDLEKSTLNE-K 190 MI D++RR+ +++ + + I + ++ E L ++ L+ + Sbjct: 140 TEMIEDVMRRTREAADQRAGAEQATAVAPRVDIDDEISIGHMLSSIEEGQLPEAELDHLR 199 Query: 191 LNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDPSKRKTGGALL 250 + K PVLG+TGTGGAGKSS+ DEL+ RFL FP+ IA+L+VDP++R++GGALL Sbjct: 200 KQWKMAGKQTPVLGVTGTGGAGKSSVVDELLLRFLHAFPDMRIAVLAVDPTRRRSGGALL 259 Query: 251 GDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVETAGIGQSDSE 310 GDRIRMNS+ RVYMRS ATR + A + + I+ LK+ +DL+IVETAGIGQSDSE Sbjct: 260 GDRIRMNSLRSHRVYMRSMATRRQHAATSVVLHDCIDFLKAQPYDLVIVETAGIGQSDSE 319 Query: 311 ITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRDVKKQFQRSRQ 370 I ++ D +YVMT +YGAA+QLEKIDM+D+A+L+ +NKFDKRGA DALRDV+KQ++R+R Sbjct: 320 IVDLVDFPMYVMTSDYGAASQLEKIDMLDFAELVVLNKFDKRGAEDALRDVRKQWKRNRT 379 Query: 371 LFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLD---WSSSYEKEEGASEKI 427 F D +PV+ TIASQFNDPG ++ N+ R L +KL L W+ + Sbjct: 380 AFALKDDEVPVYPTIASQFNDPGVTWMFANLCRLLRDKLTLPAPKWTPELDTSLKEPRAT 439 Query: 428 FIIPPDRVRYLAEIREECGRYDQFTKNESDKARK-------LFQLSGA----------IE 470 +IP RVRYLAEI E+ + + E++ A K L L A + Sbjct: 440 VLIPGSRVRYLAEIAEQGRGINAGIEREAEFASKAQHYYESLKDLGDARLPRELARYDSQ 499 Query: 471 VLKSSGQDISILKLE--YSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVS 528 L G D ++L L Y++ LS E +L W + K+ E YKVRDK I+V Sbjct: 500 SLHEEGADRTLLTLRQRYNQAVKELSHEAVHLLHDWPARYKSVTDEYNEYKVRDKTIRVE 559 Query: 529 NTTVSLSNLKIPKVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAG 588 N SLS+ KIPKV+ P+ KDWG++VR+ +EN PG +P+T GV+P++RTGEDPTRMFAG Sbjct: 560 NYRESLSHQKIPKVSPPRTKDWGDLVRFLMRENLPGYYPYTGGVYPYRRTGEDPTRMFAG 619 Query: 589 EGGPERTNARFHYVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDA 648 EG PERTN RFHY+S G A RLSTAFDSVTLYGEDP RPDIYGKIGNSGV++ATLDD Sbjct: 620 EGTPERTNRRFHYLSQGGAATRLSTAFDSVTLYGEDPAPRPDIYGKIGNSGVNVATLDDM 679 Query: 649 KKLYSGFDLCNPTTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIE-KSVRQKIES 707 KKLYSGFDL P++SVSMTINGPAP++LA FMNTAIDQ EKH+ A +QKI + Sbjct: 680 KKLYSGFDLSAPSSSVSMTINGPAPIILAMFMNTAIDQNIEKHLKADPARWAEAQQKIAA 739 Query: 708 IYKEKKFPIPKYNTQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADI 767 + P+Y+ ++P+GN+GLGL LLG+TGD++++ + Y +IK+ETL++VRGTVQADI Sbjct: 740 LQSHGG---PRYSGELPKGNEGLGLGLLGITGDQLVDAQTYARIKEETLQIVRGTVQADI 796 Query: 768 LKEDQAQNTCIFSTEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFT 827 LKEDQAQNTCIFSTEFAL+MMGDIQ++F+ ++VRNFYSVSISGYHIAEAGANPI+Q+AFT Sbjct: 797 LKEDQAQNTCIFSTEFALRMMGDIQQYFVDHKVRNFYSVSISGYHIAEAGANPISQLAFT 856 Query: 828 LANGLTYVEYFLSRGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGAND 887 L+NG T VEY+L+RGM IDDFAPNLSFFFSNG+DPEY VIGRVARRIWA+AM+ +YGA+ Sbjct: 857 LSNGFTIVEYYLARGMHIDDFAPNLSFFFSNGMDPEYTVIGRVARRIWARAMRERYGASA 916 Query: 888 RSAMLKYHIQTSGRSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESV 947 RS MLKYHIQTSGRSLHAQEI FNDIRTTLQALYA++DNCNSLHTNAYDEAITTPTEESV Sbjct: 917 RSQMLKYHIQTSGRSLHAQEIQFNDIRTTLQALYALFDNCNSLHTNAYDEAITTPTEESV 976 Query: 948 RRAMAIQLIINRELGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMM 1007 RRA+AIQLIINRELGL+ NENP QGSF+++ LTDLVE+A+ EF ISERGGVLGAM+ M Sbjct: 977 RRAVAIQLIINRELGLNFNENPWQGSFVVDALTDLVEEAVYREFEAISERGGVLGAMDTM 1036 Query: 1008 YQRNKIQEESLYYESLKHNGEFPVIGVNTFLSKEGSPTIVPQ-EVIRSTDEEKQAQISAL 1066 YQR KIQEES+YYE KH+G P+IGVNTFL K+ I + E+IRST+EEK QI + Sbjct: 1037 YQRGKIQEESMYYEQKKHDGSLPLIGVNTFLPKDHGGEIATEIELIRSTEEEKGQQIDNV 1096 Query: 1067 REFHKRNEKDIENRLRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125 + + K L+ L++ + N+F++LME K SLGQ++HALY+VGG+YRR+M Sbjct: 1097 QAYAKARNGLAPESLKILQNTARERRNVFEQLMEAVKYNSLGQISHALYDVGGEYRRNM 1155 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: 3030 Number of extensions: 135 Number of successful extensions: 7 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: 1155 Length adjustment: 46 Effective length of query: 1079 Effective length of database: 1109 Effective search space: 1196611 Effective search space used: 1196611 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