Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate CA265_RS14780 CA265_RS14780 methylmalonyl-CoA mutase
Query= BRENDA::Q8F222 (1125 letters) >lcl|FitnessBrowser__Pedo557:CA265_RS14780 CA265_RS14780 methylmalonyl-CoA mutase Length = 1129 Score = 1544 bits (3997), Expect = 0.0 Identities = 773/1135 (68%), Positives = 929/1135 (81%), Gaps = 19/1135 (1%) Query: 2 ETQIYTPKHKVRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQE 61 + +IY PK+K+RF+TAASLFDGHDA+INIMRRILQSSG EVIHLGHNRSV E+V CAIQE Sbjct: 3 QVEIYKPKNKIRFVTAASLFDGHDATINIMRRILQSSGAEVIHLGHNRSVDEVVNCAIQE 62 Query: 62 DAQGIAITSYQGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRIY 121 D QGIA+TSYQGGH+EYFKYM DLL+E+G+GHIK+F GGGG ILPSEI+EL++YG+++IY Sbjct: 63 DVQGIAMTSYQGGHIEYFKYMYDLLQERGSGHIKIFAGGGGVILPSEIEELQAYGISKIY 122 Query: 122 SPDDGRELGLQGMINDLIRRSDFIPPITFNGTLHSSLKDKNPLAIAQMITLVENTFERED 181 SPDDGR++GLQGMIND++ ++DFI + L + + K+ AIA IT+ EN + E Sbjct: 123 SPDDGRKMGLQGMINDMLVQTDFITKASITNELET-IPSKDIKAIAGAITVAEN--DPEG 179 Query: 182 LEKSTLNEKLNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDPS 241 +K ++L + P+LGITGTGGAGKSSL DELVRRFL++ +KT+AI+SVDPS Sbjct: 180 AQKFV--DELKKLSKNNTAPILGITGTGGAGKSSLVDELVRRFLVEVKDKTLAIISVDPS 237 Query: 242 KRKTGGALLGDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVET 301 KRKTGGALLGDRIRMN+I++ RVYMRS ATR+AN+AL+KNV+ SI++ K+AG+DLIIVET Sbjct: 238 KRKTGGALLGDRIRMNAINNPRVYMRSLATRQANLALSKNVQESIDICKAAGYDLIIVET 297 Query: 302 AGIGQSDSEITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRDV 361 +GIGQSD+EITE DV+LYVMTPE+GAATQLEKIDM+D+ADL+AINKFDKRGALDALRDV Sbjct: 298 SGIGQSDTEITEHCDVSLYVMTPEFGAATQLEKIDMLDFADLVAINKFDKRGALDALRDV 357 Query: 362 KKQFQRSRQLFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLDWSSSYEKEE 421 +KQ++R+ +FD D +PV+GT+ASQFNDPG N L+ ++ + K D+ + E Sbjct: 358 RKQYKRNHNIFDAKDDEIPVYGTMASQFNDPGMNNLFVALMEQIKVKTGTDFKAKMELTS 417 Query: 422 GASEKIFIIPPDRVRYLAEIREECGRYDQFTKNESDKARKLFQLSGAIEVLKSS------ 475 SEKI+IIPPDR+RYLAEI E Y+++ ++ ARK++QL G I++L + Sbjct: 418 DQSEKIYIIPPDRIRYLAEIAEASQMYNEWVDKQATIARKMYQLKGVIDLLSEANLPDKS 477 Query: 476 -----GQDISILKLEYSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVSNT 530 G D+ + Y+ E L E K++L W + + Y+ E F YKVRDKEIK Sbjct: 478 KVSPTGGDLEGV---YAFFEEQLDGECKRLLRQWPDTKRAYKEEFFIYKVRDKEIKQPLF 534 Query: 531 TVSLSNLKIPKVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAGEG 590 SLS L IPKV++P+++DWG+I+RW EN PGEFP+ +GVFP KR GEDPTRMFAGEG Sbjct: 535 YESLSKLNIPKVSLPRYEDWGDILRWLLTENLPGEFPYAAGVFPLKREGEDPTRMFAGEG 594 Query: 591 GPERTNARFHYVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDAKK 650 GPERTN RFHYVSLG PA RLSTAFDSVTLYGEDP RPDIYGKIGNSGV IATLDDAKK Sbjct: 595 GPERTNKRFHYVSLGQPAHRLSTAFDSVTLYGEDPHIRPDIYGKIGNSGVCIATLDDAKK 654 Query: 651 LYSGFDLCNPTTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIEKSVRQKIESIYK 710 LYSGFDLC P+TSVSMTINGPAPM+L FFMN AIDQ CEK+I+ + + K V KI++IY+ Sbjct: 655 LYSGFDLCAPSTSVSMTINGPAPMLLGFFMNAAIDQQCEKYIIENDLTKEVEAKIDAIYQ 714 Query: 711 EKKFPIPKYNTQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADILKE 770 K P P YN +PEGNDGLGLMLLGVTGD+VL ++Y KI+ + + VRGTVQADILKE Sbjct: 715 AKNIPRPSYNGTLPEGNDGLGLMLLGVTGDQVLPADIYAKIRTKAISSVRGTVQADILKE 774 Query: 771 DQAQNTCIFSTEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFTLAN 830 DQAQNTCIFSTEFAL+MMGDIQ++FI +VRNFYSVSISGYHIAEAGANPI+Q+AFTL+N Sbjct: 775 DQAQNTCIFSTEFALRMMGDIQKYFIDEKVRNFYSVSISGYHIAEAGANPISQLAFTLSN 834 Query: 831 GLTYVEYFLSRGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGANDRSA 890 G T+VEY+LSRGM IDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKA+K KY NDRS Sbjct: 835 GFTFVEYYLSRGMHIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAIKNKYKGNDRSQ 894 Query: 891 MLKYHIQTSGRSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRA 950 LKYHIQTSGRSLHAQEI FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRA Sbjct: 895 KLKYHIQTSGRSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRA 954 Query: 951 MAIQLIINRELGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMMYQR 1010 MAIQLIINRELGL+KNENP QG+FIIEELTDLVE A+L EF +I++RGGVLGAME MYQR Sbjct: 955 MAIQLIINRELGLAKNENPLQGAFIIEELTDLVEDAVLAEFKRINDRGGVLGAMETMYQR 1014 Query: 1011 NKIQEESLYYESLKHNGEFPVIGVNTFLSKEGSPTIVPQEVIRSTDEEKQAQISALREFH 1070 KIQEESLYYE+LKH GE+P++GVNTFL+K GSPTIVP EVIR+T++EKQ QISAL++F Sbjct: 1015 GKIQEESLYYETLKHTGEYPIVGVNTFLNKNGSPTIVPGEVIRATEDEKQYQISALQKFQ 1074 Query: 1071 KRNEKDIENRLRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125 RN + L++L+ +++ NIF++LME K SLGQ++ ALYEVGGQYRR+M Sbjct: 1075 DRNADRAVDLLKQLQKSAIAGDNIFEQLMEVCKICSLGQISKALYEVGGQYRRNM 1129 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: 3257 Number of extensions: 133 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: 1129 Length adjustment: 46 Effective length of query: 1079 Effective length of database: 1083 Effective search space: 1168557 Effective search space used: 1168557 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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