Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate H281DRAFT_02110 H281DRAFT_02110 methylmalonyl-CoA mutase
Query= BRENDA::Q8Y2U5 (1099 letters) >FitnessBrowser__Burk376:H281DRAFT_02110 Length = 1132 Score = 1521 bits (3938), Expect = 0.0 Identities = 811/1141 (71%), Positives = 898/1141 (78%), Gaps = 51/1141 (4%) Query: 1 MTDLSAARAAEPTSASEPGAVSNKVRFVTAASLFDGHDASINIMRRILQSMGCEVIHLGH 60 MTDLS + A AS ++RFVTAA+LFDGHDASINIMRRILQ+ G EVIHLGH Sbjct: 1 MTDLSTPQRA----ASHELPAGRRLRFVTAAALFDGHDASINIMRRILQASGVEVIHLGH 56 Query: 61 NRSVDEVVNAALQEDVQGIAVSSYQGGHVEYFKYMIDALRARGGEHIQVFGGGGGVIVPA 120 NRSVDEV AALQED G+AVSSYQGGH EYF+Y++D LRARGGE I+VFGGGGGVIV Sbjct: 57 NRSVDEVATAALQEDADGVAVSSYQGGHNEYFRYLVDLLRARGGERIKVFGGGGGVIVSE 116 Query: 121 EIRELQDYGVARIYSPEDGQRMGLAGMIADMVRRCDI----DLAA--------YAPTTLE 168 EI L++YGV +IYSP DGQR+GL GMI DM+ RC D A A T + Sbjct: 117 EIVALENYGVEKIYSPHDGQRLGLQGMIDDMIARCSAAAREDATARTGAVGEWLASVTGQ 176 Query: 169 PV--------AKGDR-------------RALAQLITALESGRIDPALRQAVHARAATAHT 207 P+ +G+ R LAQLI+A E+G + + R + A Sbjct: 177 PLLHLRSSAQVRGETSSADSLDASSLVFRRLAQLISAFETGGVASSKRAELSALTQAVQV 236 Query: 208 PVLGITGTGGAGKSSLTDELIRRFRLDQHDRLRIAVISIDPSRRKSGGALLGDRIRMNAI 267 PVLGITGTGGAGKSSLTDELIRRFRLD D L IAV++IDPSRRKSGGALLGDRIRMNAI Sbjct: 237 PVLGITGTGGAGKSSLTDELIRRFRLDYGDTLTIAVLAIDPSRRKSGGALLGDRIRMNAI 296 Query: 268 NH----PNLFVRSLATREASSEISDALPDVIAACRAGGFDLIIVETSGIGQGDAAIVPHA 323 +++RS+ATREASSEISDALPD + C+A GFDLI+VETSGIGQGDAAIVP Sbjct: 297 GDWGGGARVYMRSMATREASSEISDALPDALMLCKAAGFDLIVVETSGIGQGDAAIVPFV 356 Query: 324 DLSLYVMTPEFGAASQLEKIDMLDFADLVAINKFDRKGAQDAWRDVAKQVQRNREQWHAK 383 D SLYVMTPEFGAASQLEKIDMLDFAD VAIN+FDRKGA DA RDVAKQVQRNR + Sbjct: 357 DESLYVMTPEFGAASQLEKIDMLDFADAVAINRFDRKGAPDALRDVAKQVQRNRADFAKS 416 Query: 384 PEDMPVFGTQASHFNDDGVTALYHALADRLAERGMALAERTLPRPAGT-CSTSHDAIVPP 442 PE MPVFGT ASHFNDDGVTALY +A+ L + G+ L A S+ AIVPP Sbjct: 417 PEAMPVFGTIASHFNDDGVTALYQYIAEALRKHGLRSGGGRLSIAADVRFSSGRHAIVPP 476 Query: 443 ARVRYLAEVADTVRGYHRRVDAQSGLARERQQLQASRRML-EAAGAAADV---LTALDAQ 498 ARVRYLAE+A T+ Y RVD Q+G+ARER QL +RRML EA+ A D L +LDA Sbjct: 477 ARVRYLAEIAQTIHAYRERVDQQAGVARERWQLVEARRMLGEASADAHDAQASLASLDAL 536 Query: 499 AAERDARLGAAERKLLAMWPDLRRAYAGDEYVVKIRDRELRTPLTYTTLSGTTLRKVVLP 558 +R LG ERKLL WP AY+GD++VV+IRDRE+RT LT TTLSGT LRKV LP Sbjct: 537 IEQRTTALGEHERKLLDAWPQTVAAYSGDDHVVRIRDREIRTALTATTLSGTQLRKVALP 596 Query: 559 PYEDDGEILRWLMRENVPGSFPYTAGVFAFKRRGDVGGEDPTRMFAGEGDALRTNRRFKL 618 + D GEILRWLM +N+PG FP+TAGVF F+R EDPTRMFAGEGD RTNRRFKL Sbjct: 597 KFVDHGEILRWLMLDNLPGYFPFTAGVFPFRREN----EDPTRMFAGEGDPSRTNRRFKL 652 Query: 619 VSEGMEAKRLSTAFDSVTLYGEDPDPRPDIYGKVGNAGVSIATLDDLKVLYDGFDLTSPN 678 +SEGM AKRLSTAFDSVTLYGE+PD RPDIYGKVGN+GVS+ATLDD+ LYDGFDL +P Sbjct: 653 LSEGMPAKRLSTAFDSVTLYGEEPDERPDIYGKVGNSGVSVATLDDMHALYDGFDLCAPQ 712 Query: 679 TSVSMTINGPAPTILAMFMNTALDQNLARFRADNGREPTEGEEAKIRAWVLQNVRGTVQA 738 TSVSMTINGPAPTILAMF N A+DQ +AR GR +E E A+ R L+NVRGTVQA Sbjct: 713 TSVSMTINGPAPTILAMFFNVAIDQQIARQAQQLGRALSEDELAETRRMALENVRGTVQA 772 Query: 739 DILKEDQGQNTCIFSTAFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLA 798 DILKEDQGQNTCIFST FSLKVMGDIQ YFV H+VRNFYSVSISGYHIAEAGANPISQLA Sbjct: 773 DILKEDQGQNTCIFSTEFSLKVMGDIQAYFVEHRVRNFYSVSISGYHIAEAGANPISQLA 832 Query: 799 FTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGA 858 +TLANGFTYVEAYLARGM IDDFAPNLSFFFSNGMDPEY+VLGRVARR+WA+ MR++YGA Sbjct: 833 YTLANGFTYVEAYLARGMSIDDFAPNLSFFFSNGMDPEYTVLGRVARRVWAIAMRERYGA 892 Query: 859 NERSQKLKYHVQTSGRSLHAQEIAFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAE 918 NERSQKLKYHVQTSGRSLHAQEI FNDIRTTLQALIAIYDNCNSLHTNA+DEAITTPT E Sbjct: 893 NERSQKLKYHVQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAFDEAITTPTEE 952 Query: 919 SVRRALAIQLIINREWGLAKCENPNQGSFIIDELTDLVEAAVLREFERLAERGGVLGAME 978 SVRRA+AIQLIINREWGLAK +NPNQGSF+IDELTDLVE AVL EF+RL ERGGVLGAME Sbjct: 953 SVRRAVAIQLIINREWGLAKNQNPNQGSFVIDELTDLVEEAVLAEFDRLTERGGVLGAME 1012 Query: 979 TGYQRGRIQEESMLYEQRKHDGSLPIVGVNTFRNPEAGHAAPAHIELARSSEEEKQRQLA 1038 TGYQRGRIQ+ESMLYE RKHDGS PIVGVNTF + + H AP I LARS+EEEKQ QL Sbjct: 1013 TGYQRGRIQDESMLYEHRKHDGSYPIVGVNTFVSAKP-HEAPTPIALARSTEEEKQSQLK 1071 Query: 1039 RLADFHARHAAEAPAMLQRLQRAVIDDQNVFAVLMDAVRVCSLGQITHALFEVGGQYRRN 1098 RL DF ARH APA L+RLQRAVIDD+NVFAVLMD VRVCSLGQITHALFEVGGQYRRN Sbjct: 1072 RLRDFQARHRGAAPAALERLQRAVIDDENVFAVLMDVVRVCSLGQITHALFEVGGQYRRN 1131 Query: 1099 M 1099 M Sbjct: 1132 M 1132 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: 2995 Number of extensions: 115 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 1099 Length of database: 1132 Length adjustment: 46 Effective length of query: 1053 Effective length of database: 1086 Effective search space: 1143558 Effective search space used: 1143558 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 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