Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate CCNA_02459 CCNA_02459 methylmalonyl-CoA mutase alpha subunit
Query= BRENDA::P11653 (728 letters) >FitnessBrowser__Caulo:CCNA_02459 Length = 714 Score = 984 bits (2543), Expect = 0.0 Identities = 500/727 (68%), Positives = 578/727 (79%), Gaps = 19/727 (2%) Query: 1 MSTLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDW 60 MST P F + P PA A GEAW T E + V F+ +D+ Sbjct: 1 MSTFPDFTKIAFAEVPAPA------------APKGEAWNTPEGVAVAPAFDASDVAGLDF 48 Query: 61 LDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLP 120 + G+ PFV GPY TMY PWT+RQYAGFSTA++SNAFYRRNLAAGQ GLSVAFDL Sbjct: 49 TGGFPGVAPFVRGPYPTMYVTNPWTVRQYAGFSTAEDSNAFYRRNLAAGQMGLSVAFDLA 108 Query: 121 THRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVV 180 THRGYDSD+ RV GDVGMAGVAIDSI DMR LF+GIPLD+MSVSMTMNGAVLPILALY+V Sbjct: 109 THRGYDSDHERVKGDVGMAGVAIDSILDMRTLFSGIPLDKMSVSMTMNGAVLPILALYIV 168 Query: 181 TAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISI 240 AEEQGV P++L+GTIQNDILKEFMVRNTYIYPP PSMRIIS+IFA+TSANMPK+NSISI Sbjct: 169 AAEEQGVSPDKLSGTIQNDILKEFMVRNTYIYPPAPSMRIISDIFAFTSANMPKFNSISI 228 Query: 241 SGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAK 300 SGYHMQEAGATAD+E+AYTLADGV+Y RAG + G+++DQFAPRLSFFW IGMN+FMEVAK Sbjct: 229 SGYHMQEAGATADLELAYTLADGVEYARAGVAAGMSIDQFAPRLSFFWAIGMNYFMEVAK 288 Query: 301 LRAARMLWAKLV-HQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGH 359 +RAAR+LWA+L+ +F PK+ +S+SLRTHSQTSGWSL AQDV+NNV RTC+EAMAA G Sbjct: 289 MRAARLLWARLMKREFDPKDDRSLSLRTHSQTSGWSLAAQDVFNNVARTCVEAMAAVNGQ 348 Query: 360 TQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARK 419 TQSLHTNSLDEA+ALPTDFSARI+RNTQLFLQ ESGTTRV DPW GS YVE LT++LA+K Sbjct: 349 TQSLHTNSLDEALALPTDFSARISRNTQLFLQMESGTTRVADPWGGSYYVERLTYELAQK 408 Query: 420 AWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLD 479 A HI+EVE +GGMAKAIE+G+PK+RIEEAAARTQARIDSG+Q ++GVN+Y+ E + Sbjct: 409 ALAHIEEVEALGGMAKAIEQGLPKLRIEEAAARTQARIDSGKQSVVGVNRYKPEVADDIP 468 Query: 480 VLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAG 539 VLKVDN V A+Q KL +L+AERDP +AAL + D D NLL L +DA Sbjct: 469 VLKVDNGAVRAQQLEKLARLKAERDPAATEAALTAL------EDGARGDGNLLALAVDAA 522 Query: 540 RAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPR 599 RA ATVGE+S ALEKVFGR+ A+I++I GVY KE N P A+ +VE FEQA+GRRPR Sbjct: 523 RAKATVGEISYALEKVFGRHRAEIKSIQGVYMKEAGNDPTAARAKAMVEAFEQADGRRPR 582 Query: 600 ILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAG 659 IL+AKMGQDGHDRGQKVIATA+ADLGFDVD+GPLFQTP E ARQAVE DVHVVG SSLA Sbjct: 583 ILIAKMGQDGHDRGQKVIATAFADLGFDVDIGPLFQTPAEAARQAVENDVHVVGASSLAA 642 Query: 660 GHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLV 719 GHLTL P L+ EL K GR DIL+ VGGVIP QDF LR GA I+ PGTVI E+AI L+ Sbjct: 643 GHLTLAPELKAELAKQGRDDILMVVGGVIPPQDFQALRDAGAAAIFPPGTVIAEAAIELL 702 Query: 720 KKLRASL 726 ++L L Sbjct: 703 EQLNRQL 709 Lambda K H 0.317 0.133 0.389 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: 1413 Number of extensions: 49 Number of successful extensions: 4 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: 728 Length of database: 714 Length adjustment: 40 Effective length of query: 688 Effective length of database: 674 Effective search space: 463712 Effective search space used: 463712 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