Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate WP_011842539.1 RSPH17029_RS18485 methylmalonyl-CoA mutase family protein
Query= BRENDA::O74009 (563 letters) >NCBI__GCF_000015985.1:WP_011842539.1 Length = 563 Score = 570 bits (1470), Expect = e-167 Identities = 285/562 (50%), Positives = 395/562 (70%), Gaps = 3/562 (0%) Query: 3 TFDKEVLKKIKEEEKRWEETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPADLGEDWNYM 62 TF +I + + WE T V F+ +APERKE+F T F +KR YT AD+ + + Sbjct: 4 TFSHARTDEIAQAVEDWERTEVADFIARAPERKEQFYTLGDFPVKRTYTAADIAD--TPL 61 Query: 63 EKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYLLSQGQTGLSVAFDL 122 E +G PG+YPFTRG Y TMYRGR WTMRQ AG+ T E++NKR+K+L+ QGQTG+S FD+ Sbjct: 62 EDIGLPGKYPFTRGPYPTMYRGRNWTMRQIAGFGTGEDTNKRFKFLIEQGQTGISTDFDM 121 Query: 123 PTQLGYDSDHPLAEGEVGKVGVAIDSLWDMRILFDGIPLDKVSTSMTINSTAANLLAMYI 182 PT +GYDSDHP+++GEVG+ GVAID+L DMR L DGI L+K+S S+TIN TA LLAMYI Sbjct: 122 PTLMGYDSDHPMSDGEVGREGVAIDTLADMRALLDGIDLEKISVSLTINPTAWILLAMYI 181 Query: 183 LVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCAENVPKWNPIS 242 + EE+G K+ GTVQ DILKEY+A+ YIFP PS+R+ DII + + ++NPI+ Sbjct: 182 ALCEERGYDLNKVSGTVQADILKEYMAQKEYIFPIAPSVRIVRDIISHSTRTMKRYNPIN 241 Query: 243 ISGYHIREAGANAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIA 302 ISGYHI EAG++ + E AFTLA+ I YV+ V++ G++VD FAPRL+FFF +F EEIA Sbjct: 242 ISGYHISEAGSSPLHEAAFTLANLIVYVEEVLKTGVEVDDFAPRLAFFFVCQADFFEEIA 301 Query: 303 KFRAARRLWAYIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLG 362 KFRA RR +A IMKE F AK P SM LRFH QTA ++LT Q N++R QALAAVLG Sbjct: 302 KFRALRRCYAKIMKERFGAKKPESMRLRFHCQTAAASLTKPQYMVNVMRTTTQALAAVLG 361 Query: 363 GTQSLHTNSYDEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYE 422 G QSLHTN YDEA ++PTE ++++ALRTQQ+IA E+GV VDPLGG+Y++E LT+ + Sbjct: 362 GAQSLHTNGYDEAFAIPTEHAMQLALRTQQVIADETGVTQVVDPLGGSYFVESLTNDYEK 421 Query: 423 EALKYIEKIQKMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEP-IE 481 + + ++++++ GG ++ IE G+ QK IA+ AY+ + G++ ++GVN +V DE ++ Sbjct: 422 KIFEILDEVEERGGAIKLIEEGWFQKHIADFAYETALRKQSGEKPVIGVNRYVMDESHVK 481 Query: 482 VEILKVDPSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLA 541 +E+ D + ++QI+R + +R+ RD KVQ LD+L A E N+MP I+ + A Sbjct: 482 IEVHPYDETTAKRQIDRTRSVRAGRDEAKVQALLDELVAVARDESANVMPVTIQLVKEGA 541 Query: 542 TLQEVTDVLREIWGEYRAPLIF 563 T+ ++ + L+ IWG YR +F Sbjct: 542 TMGDIVEKLKTIWGVYRETPVF 563 Lambda K H 0.318 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: 800 Number of extensions: 30 Number of successful extensions: 3 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: 563 Length of database: 563 Length adjustment: 36 Effective length of query: 527 Effective length of database: 527 Effective search space: 277729 Effective search space used: 277729 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: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. 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