Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_036834456.1 N784_RS09590 methylmalonyl-CoA mutase family protein
Query= BRENDA::Q8Y2U5 (1099 letters) >NCBI__GCF_000775615.1:WP_036834456.1 Length = 1079 Score = 1289 bits (3335), Expect = 0.0 Identities = 663/1080 (61%), Positives = 812/1080 (75%), Gaps = 17/1080 (1%) Query: 25 VRFVTAASLFDGHDASINIMRRILQSMGCEVIHLGHNRSVDEVVNAALQEDVQGIAVSSY 84 VRFVTA+SLFDGHDASINIMRRILQ+ G EVIHLGHNRSV+EVVNAA+QED QGIA+SSY Sbjct: 12 VRFVTASSLFDGHDASINIMRRILQASGAEVIHLGHNRSVEEVVNAAIQEDAQGIAMSSY 71 Query: 85 QGGHVEYFKYMIDALRARGGEHIQVFGGGGGVIVPAEIRELQDYGVARIYSPEDGQRMGL 144 QGGHVEYFKYMID L+A+G +HI+V+GGGGGVI+P EI+EL DYGVARI+SPEDG+ GL Sbjct: 72 QGGHVEYFKYMIDLLKAKGADHIRVYGGGGGVIIPREIKELHDYGVARIFSPEDGREYGL 131 Query: 145 AGMIADMVRRCDIDLAAYAPTTLEPVAKGDRRALAQLITALESGRI---DPALRQAVHAR 201 GMI M+ CD + ++ + +GD +A+A+ IT E+ I +PA Sbjct: 132 QGMINQMIEACDFQPPLHVEQHMQQLQQGDSQAIARFITYTENTTIHETEPAAAVEKLLE 191 Query: 202 AATAHTPVLGITGTGGAGKSSLTDELIRRFRLDQHDRLRIAVISIDPSRRKSGGALLGDR 261 T PVLGITGTGGAGKSSLTDELIRRF L++ ++A++S+DP++RK+GGALLGDR Sbjct: 192 QQTKSIPVLGITGTGGAGKSSLTDELIRRF-LNEIPERKVAILSVDPTKRKTGGALLGDR 250 Query: 262 IRMNAINHPNLFVRSLATREASSEISDALPDVIAACRAGGFDLIIVETSGIGQGDAAIVP 321 IRMNAI +++RSLATR++ SE+S ++ + I +A GFDLI+VETSGIGQGDAA+ Sbjct: 251 IRMNAIFSDRVYMRSLATRDSRSELSKSIDEAIQVVKAAGFDLIVVETSGIGQGDAAVTD 310 Query: 322 HADLSLYVMTPEFGAASQLEKIDMLDFADLVAINKFDRKGAQDAWRDVAKQVQRNREQWH 381 DLS+YVMT EFGA SQLEKIDM+D+AD + INKF++KG+ DA R V KQ +R+ +H Sbjct: 311 VTDLSMYVMTAEFGAPSQLEKIDMIDYADFIVINKFEQKGSADALRQVRKQYERSHMLFH 370 Query: 382 AKPEDMPVFGTQASHFNDDGVTALYHALADRLAER-GMALAERTLPRPAGTCSTSHDAIV 440 P++GT AS FND G L+ AL D + ++ G E + P T + I+ Sbjct: 371 EDQTTFPIYGTIASQFNDPGTNTLFAALVDLINDKYGW---EESTPFERVTNVEKQNLII 427 Query: 441 PPARVRYLAEVADTVRGYHRRVDAQSGLARERQQLQASRRMLEAAGAAADVLTALDAQAA 500 PP R +YL ++ TV YH + + QS AR+ QL S ++E +LT AA Sbjct: 428 PPERQQYLRDIVQTVHHYHEKAEEQSDKARKWYQLTKSANLIEEETMKQQLLTT----AA 483 Query: 501 ERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIRDRELRTPLTYTTLSGTTLRKVVLPPY 560 + +L ++ L W DL+ Y+ + +R++E+ LT +LSG + KV LP Y Sbjct: 484 HYEHQLDPNHKQTLEQWDDLKHRYSQEVMTYAVRNKEITIDLTTESLSGLQIPKVALPTY 543 Query: 561 EDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDVGGEDPTRMFAGEGDALRTNRRFKLVS 620 D G+ L W++REN+PG+FP+TAGVF FKR+G EDPTR FAGEG RTNRRF +S Sbjct: 544 HDWGDRLLWVLRENIPGAFPFTAGVFPFKRKG----EDPTRQFAGEGTPDRTNRRFHYLS 599 Query: 621 EGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGNAGVSIATLDDLKVLYDGFDLTSPNTS 680 EG AKRLSTAFDSVTLYGEDPD RPDIYGKVG +GVSI TLDD++ LY GFDL P TS Sbjct: 600 EGEAAKRLSTAFDSVTLYGEDPDERPDIYGKVGESGVSICTLDDMQKLYAGFDLCHPTTS 659 Query: 681 VSMTINGPAPTILAMFMNTALDQNLARFRADNGREPTEGEEAKIRAWVLQNVRGTVQADI 740 VSMTINGPAP ILAMF NTA+DQ + F+ GREP + E +I+A + VRGTVQADI Sbjct: 660 VSMTINGPAPIILAMFFNTAIDQQIEMFKKQEGREPNQEERDRIKAETISVVRGTVQADI 719 Query: 741 LKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFT 800 LKEDQGQNTCIFST F+L++MGDIQ+YF+ H V+N+YSVSISGYHIAEAGANPI+QLAFT Sbjct: 720 LKEDQGQNTCIFSTEFALRMMGDIQQYFIDHDVKNYYSVSISGYHIAEAGANPITQLAFT 779 Query: 801 LANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGANE 860 LANGFTYVE YL+RGM I+ FAPNLSFFFSNG+DPEY+V+GRVARRIWA+ MRDKYGANE Sbjct: 780 LANGFTYVEYYLSRGMDINKFAPNLSFFFSNGLDPEYTVIGRVARRIWAIVMRDKYGANE 839 Query: 861 RSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESV 920 RSQKLKYHVQTSGRSLHAQEI FNDIRTTLQAL+AI DNCNSLHTN+YDEAITTPT ESV Sbjct: 840 RSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALLAIQDNCNSLHTNSYDEAITTPTEESV 899 Query: 921 RRALAIQLIINREWGLAKCENPNQGSFIIDELTDLVEAAVLREFERLAERGGVLGAMETG 980 RRA+AIQ+IIN+E+GL K EN QGSFI++ELT LVE AVL+EFER+ +RGGVLGAME Sbjct: 900 RRAMAIQMIINKEFGLTKNENSLQGSFIVEELTHLVEEAVLQEFERMNDRGGVLGAMERQ 959 Query: 981 YQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPEAGHAAPA-HIELARSSEEEKQRQLAR 1039 YQRG+IQEES+ YE +KH G LPI+GVNT+ NP +ELAR+S+EEK Q+ Sbjct: 960 YQRGKIQEESLYYEGKKHSGDLPIIGVNTYLNPNPPSEEDIDSMELARASQEEKMHQIHS 1019 Query: 1040 LADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMDAVRVCSLGQITHALFEVGGQYRRNM 1099 L DF R+A LQRL++ + N+FA LM+ V+V SLGQIT+AL+EVGGQYRRNM Sbjct: 1020 LRDFQERNAQVTENALQRLKQVAKQNGNIFAELMETVKVASLGQITNALYEVGGQYRRNM 1079 Lambda K H 0.320 0.134 0.388 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: 2659 Number of extensions: 97 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: 1099 Length of database: 1079 Length adjustment: 46 Effective length of query: 1053 Effective length of database: 1033 Effective search space: 1087749 Effective search space used: 1087749 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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