Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate AZOBR_RS24250 AZOBR_RS24250 methylmalonyl-CoA mutase
Query= BRENDA::Q84FZ1 (721 letters) >FitnessBrowser__azobra:AZOBR_RS24250 Length = 732 Score = 1080 bits (2793), Expect = 0.0 Identities = 546/729 (74%), Positives = 622/729 (85%), Gaps = 14/729 (1%) Query: 5 IPDFASVAYAADGFKAPPP-------------PAGEPWMTPEGIPVKGFYGPEDREGCEG 51 +PDF+++ A A P PA W TPE + VK Y D +G + Sbjct: 4 LPDFSTLPLDAAVSNASPAEWSRRFAAETGTDPATALWRTPEMLDVKPLYTAADLDGLDH 63 Query: 52 IDSFPGLPPYLRGPYPAMYVTQPWTIRQYAGFSTAEDSNAFYRRNLAAGQKGLSVAFDLA 111 + + PG+ P+LRGPYP MYV +PWT+RQYAGFSTA++SNAFYRRNLAAGQKGLSVAFDLA Sbjct: 64 LAAMPGMAPFLRGPYPTMYVDKPWTVRQYAGFSTAQESNAFYRRNLAAGQKGLSVAFDLA 123 Query: 112 THRGYDSDHPRVSGDVGMAGVAIDSIYDMRTLFSGIPLDEMTVSMTMNGAVLPGVALYIV 171 THRGYDSDHPRV+GDVGMAGVAIDSI DM+TLF GIPLD+M+VSMTMNGAVLP +A YIV Sbjct: 124 THRGYDSDHPRVTGDVGMAGVAIDSILDMKTLFDGIPLDQMSVSMTMNGAVLPVLAGYIV 183 Query: 172 AAEEQGVPPEKLAGTIQNDILKEFMVRNTYIYPPKGSMRIISDIFGYTSKNMPKFNSISI 231 AAEEQGV +KL+GTIQNDILKEFMVRNTYIYPPK SMRIISDIF +TS++MPKFNSISI Sbjct: 184 AAEEQGVSADKLSGTIQNDILKEFMVRNTYIYPPKPSMRIISDIFAFTSQHMPKFNSISI 243 Query: 232 SGYHMQEAGATQDLELAYTLADGVEYIKAGLAAGLTIDQFAPRLSFFWAIGMNFFMEIAK 291 SGYH+QEAGAT DLELAYTLADGVEY +AGLAAGLTIDQFAPRLSFFWAIGMNFFME+AK Sbjct: 244 SGYHLQEAGATADLELAYTLADGVEYARAGLAAGLTIDQFAPRLSFFWAIGMNFFMEVAK 303 Query: 292 MRAARLIWAKLVKEFEPKSDKSLPLRTHSQTSGWSLTAQDVFNNVTRTCIEAMAATQGGT 351 MRA R++WAKL+KEF PKSDKSL LRTHSQTSGWSLTAQDVFNNVTRTCIEAMA+TQG T Sbjct: 304 MRAGRMLWAKLIKEFAPKSDKSLSLRTHSQTSGWSLTAQDVFNNVTRTCIEAMASTQGHT 363 Query: 352 QSLHTNALDEALALPTDFSARIARNTQLFLQQESGTTRIIDPWGGSYYVERLTRDIAARA 411 QSLHTNALDEALALPTDFSARIARNTQLFLQQESGT R+IDPWGGSYYVERLTR++AARA Sbjct: 364 QSLHTNALDEALALPTDFSARIARNTQLFLQQESGTCRVIDPWGGSYYVERLTRELAARA 423 Query: 412 WEHIREVEALGGMAKAIEAGIPKLRIEEAAARAQARIDSGRQTIVGINKYKPDDEMKIDL 471 W HIREVE GGMAKAIE GIPK+R+EEAAAR QARIDSGRQT+VG+NKY+ + E I++ Sbjct: 424 WGHIREVEETGGMAKAIETGIPKMRVEEAAARTQARIDSGRQTVVGVNKYRLEQEEAIEV 483 Query: 472 LRVDNADVRAKQIDKLKRLRAERNQADVDAALAALTK-AADGEGNLLELAVNAARAKATV 530 L+VDN+ VRA+QI +L+RLRAER+ L ALT AA G+GNLL L+V+A RA+ATV Sbjct: 484 LKVDNSAVRAQQIAQLERLRAERDPIRCRQTLEALTNAAAAGDGNLLALSVDAIRARATV 543 Query: 531 GEISEALEKAWGRHRAQIRSISGVYKREVGGMSPVVEKVRGLVEAFEENDGRRPRILVAK 590 GEIS+ALEK +GRH+A+IR+I+G+Y EVG S + +VR LV F E DGRRPRI+VAK Sbjct: 544 GEISDALEKVYGRHKAEIRTITGIYAGEVGRQSDAIARVRALVAEFAERDGRRPRIMVAK 603 Query: 591 MGQDGHDRGQKVIASAFADLGFDVDIGPLFATPDEAARQAVENDVHIVGVSSLAAGHLTL 650 MGQDGHDRGQKVIA+AFADLGFDVD+GPLF TP+EAARQAVEND HIVGVSSLAAGHLTL Sbjct: 604 MGQDGHDRGQKVIATAFADLGFDVDVGPLFQTPEEAARQAVENDCHIVGVSSLAAGHLTL 663 Query: 651 VPELKAALKQEGRDDVMIVVGGVIPPGDYDALYAAGASAIFPPGTVIAEAAVNLLGELNT 710 VP+LKA L++ G D++IVVGGV+PP DYDALYAAGA+AIFPPGTVI+EAAV+LL LN Sbjct: 664 VPQLKAELERHGAGDILIVVGGVVPPQDYDALYAAGATAIFPPGTVISEAAVDLLRILNE 723 Query: 711 RLGYGERQA 719 R GY + A Sbjct: 724 RHGYAPKAA 732 Lambda K H 0.318 0.134 0.391 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: 1398 Number of extensions: 37 Number of successful extensions: 2 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: 721 Length of database: 732 Length adjustment: 40 Effective length of query: 681 Effective length of database: 692 Effective search space: 471252 Effective search space used: 471252 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 (21.7 bits) S2: 55 (25.8 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