Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_065399519.1 BBI00_RS15060 methylmalonyl-CoA mutase family protein
Query= BRENDA::Q8F222 (1125 letters) >NCBI__GCF_001684965.1:WP_065399519.1 Length = 1115 Score = 1468 bits (3800), Expect = 0.0 Identities = 735/1125 (65%), Positives = 902/1125 (80%), Gaps = 10/1125 (0%) Query: 1 METQIYTPKHKVRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQ 60 METQ YTP +KVR +TAASLFDGHDA+INIMRR++Q +G EVIHLGH++S E+V AIQ Sbjct: 1 METQKYTPTNKVRIVTAASLFDGHDAAINIMRRVIQGTGCEVIHLGHDKSAEEVVNTAIQ 60 Query: 61 EDAQGIAITSYQGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRI 120 EDA IA+TSYQGGH EYFKY+ DLL+EK + IK+FGGGGG ILP EIK+L SYG+ RI Sbjct: 61 EDANAIALTSYQGGHNEYFKYIYDLLREKNSPQIKIFGGGGGVILPEEIKDLMSYGIDRI 120 Query: 121 YSPDDGRELGLQGMINDLIRRSDFIPPITFNGTLHSSLKDKNPLAIAQMITLVENTFERE 180 YSPDDGRELGLQGMI+DL+ RSDF + +NP +IAQ+I+ VEN E Sbjct: 121 YSPDDGRELGLQGMIDDLVHRSDFATGKDVTAKDLDDISFENPSSIAQIISAVENFSE-- 178 Query: 181 DLEKSTLNEKLNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDP 240 EK L + ++ ++P++GITGTGGAGKSSLTDELVRRFL +K IAI+S+DP Sbjct: 179 --EKPELVKAIDEESKHLNIPIIGITGTGGAGKSSLTDELVRRFLRSNTDKKIAIISIDP 236 Query: 241 SKRKTGGALLGDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVE 300 SK+KTGGALLGDRIRMN+I+ RVYMRS ATRE N++++ + ++ VLK A D+II+E Sbjct: 237 SKKKTGGALLGDRIRMNAINDPRVYMRSMATRENNVSVSPFIHSALNVLKLAHPDVIILE 296 Query: 301 TAGIGQSDSEITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRD 360 T+GIGQS SE+++ ADV++YVMTPEYGA+TQLEKIDM+DYADL+A+NK DKRGALDAL+ Sbjct: 297 TSGIGQSGSEVSDFADVSMYVMTPEYGASTQLEKIDMLDYADLVALNKSDKRGALDALQA 356 Query: 361 VKKQFQRSRQLFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLDWSSSYEKE 420 V+KQFQR+ L++ +D MPV+ T ASQFND GT LY ++ ++ K + S E Sbjct: 357 VRKQFQRNHLLWESPLDDMPVYATKASQFNDHGTTELYNRLVSKVNEKFP-ELSLKTFVE 415 Query: 421 EGASEKIFIIPPDRVRYLAEIREECGRYDQFTKNESDKARKLFQLSGAIEVLKSSGQDIS 480 + +E++ IIPP RVRYL+EI E +YD + +++ ARK++ + G ++ + Sbjct: 416 QEVTEEVTIIPPKRVRYLSEIVENNKQYDANIEKQAELARKMYHIEGVKAIISNE----- 470 Query: 481 ILKLEYSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVSNTTVSLSNLKIP 540 +L+ EY K E L E L +W++ K + E ++Y VR KEIKV +T SLS+L+IP Sbjct: 471 VLEAEYQKAEKELQQENIDFLKTWDDTKKAFHAEFYSYFVRGKEIKVETSTESLSHLRIP 530 Query: 541 KVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAGEGGPERTNARFH 600 K+A+PK+ DWG++++W QEN PG FP+T+G++PFKRTGEDPTRMFAGEGGPERTN RFH Sbjct: 531 KIALPKYNDWGDLIKWKGQENLPGSFPYTAGIYPFKRTGEDPTRMFAGEGGPERTNRRFH 590 Query: 601 YVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDAKKLYSGFDLCNP 660 YVS MPA+RLSTAFDSVTLYG+DP PDIYGKIGN+GVSIATLDDAKKLYSGFDL N Sbjct: 591 YVSAEMPAKRLSTAFDSVTLYGQDPALPPDIYGKIGNAGVSIATLDDAKKLYSGFDLVNA 650 Query: 661 TTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIEKSVRQKIESIYKEKKFPIPKYN 720 TSVSMTINGPAPM+LAFFMN AIDQ EK+I +G+E V K++ + +K PKYN Sbjct: 651 LTSVSMTINGPAPMLLAFFMNAAIDQNVEKYIKENGLEAKVEAKLKEKFDDKGLERPKYN 710 Query: 721 TQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADILKEDQAQNTCIFS 780 ++P N+GLGL LLG+TGDEV+ +VY +IK +T+ VRGTVQADILKEDQAQNTCIFS Sbjct: 711 GELPPSNNGLGLQLLGLTGDEVIPADVYAEIKAKTIATVRGTVQADILKEDQAQNTCIFS 770 Query: 781 TEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFTLANGLTYVEYFLS 840 TEFAL++MGD+QE+FIK +VRNFYSVSISGYHIAEAGANP++Q+AFTLANG TYVEY+LS Sbjct: 771 TEFALRLMGDVQEYFIKEKVRNFYSVSISGYHIAEAGANPVSQLAFTLANGFTYVEYYLS 830 Query: 841 RGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGANDRSAMLKYHIQTSG 900 RGM I+DFAPNLSFFFSNGIDPEY+VIGRVARRIWAKAMK KYGA++RS MLKYHIQTSG Sbjct: 831 RGMDINDFAPNLSFFFSNGIDPEYSVIGRVARRIWAKAMKLKYGADERSQMLKYHIQTSG 890 Query: 901 RSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRAMAIQLIINRE 960 RSLHAQEI FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTE+SVRRAMAIQLIIN+E Sbjct: 891 RSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEQSVRRAMAIQLIINKE 950 Query: 961 LGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMMYQRNKIQEESLYY 1020 LGL+KNENP QGSFIIEELTDLVE+A+ EF +I+ERGGVLGAME MYQR+KIQEES++Y Sbjct: 951 LGLAKNENPLQGSFIIEELTDLVEEAVYTEFDRITERGGVLGAMETMYQRSKIQEESMHY 1010 Query: 1021 ESLKHNGEFPVIGVNTFLSKEGSPTIVPQEVIRSTDEEKQAQISALREFHKRNEKDIENR 1080 E LKH GE+P+IGVNTFL K+GSPT++P EVIRST+EEKQAQI L F K NE E Sbjct: 1011 EWLKHTGEYPIIGVNTFLGKDGSPTVLPGEVIRSTEEEKQAQIEFLHNFQKANESKSEEA 1070 Query: 1081 LRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125 LR L+ +++ N+F+ +M+ K SLGQ+T+AL+EVGG+YRR+M Sbjct: 1071 LRTLQHAAINQQNLFEVMMDAVKYCSLGQITNALFEVGGKYRRNM 1115 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: 3179 Number of extensions: 130 Number of successful extensions: 5 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: 1115 Length adjustment: 46 Effective length of query: 1079 Effective length of database: 1069 Effective search space: 1153451 Effective search space used: 1153451 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 24 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