Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate RR42_RS01335 RR42_RS01335 methylmalonyl-CoA carboxyltransferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2192 (535 letters) >FitnessBrowser__Cup4G11:RR42_RS01335 Length = 515 Score = 181 bits (458), Expect = 8e-50 Identities = 157/522 (30%), Positives = 255/522 (48%), Gaps = 54/522 (10%) Query: 38 QGGGPKAQERHTSRGKLLPRERINRLLDPGSPFLEISPLAAHEVYGED-----VPAAGVI 92 Q GGP +RH GKL RERI+ + D GS F E+ L Y + + A ++ Sbjct: 19 QLGGPDKVKRHKDAGKLTVRERIDAIADAGS-FREVGALTGSGQYDSNGRLVGLTPANLV 77 Query: 93 AGIGRVEGVECMIVANDATVKGGSYYPLTVKKHLRAQTIAQQNRLPCIYLVD-SGGANLP 151 G +V+G ++V +D TV+GG+ +K + A+ +A RLP + LVD +GG Sbjct: 78 MGRAKVDGRPVVLVGDDFTVRGGANDGAVGEKLIHAEKMAHDLRLPMVRLVDGTGGGGSV 137 Query: 152 RQDEV-----FPDREHFGRIFFNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADEAIMVR 206 R E P + + + NMS +P +++ +GS GA A + ++MV+ Sbjct: 138 RNIENKGYTNIPTMKVWQHVV---ENMSL--VPVVSLALGSVAGMGAARVAASHYSVMVK 192 Query: 207 QQATIFLAGPPLVKAATGEVVSAEDLGGADVHCKISGVADHYADSDEHALALARRSVANL 266 A +F AGPP+V A G+V+ +LGG+ +H + +GV D S+E A A ARR ++ L Sbjct: 193 GTAQLFNAGPPVV-ARIGQVLEKNELGGSQIHTR-NGVVDDEVASEEEAFARARRFLSYL 250 Query: 267 NWRKQGELQHRLPIA------PLYSGEELYGVVSADAKQPFDVREVIARLVDGSVFDEFK 320 G + H LP P E L + D++ + VR ++ LVD F E Sbjct: 251 ----PGSV-HELPPRVEPTDDPARRDEWLLSAIPRDSRSVYKVRPIVETLVDQGSFFEMG 305 Query: 321 ALFGTTLVCGFAHLHGYPIAILANNGILFA-----EAAQKGAHFIELACQRGIPLLFLQN 375 +G +V G A + G+P+A++A++ + A+K F++LA +P++ + + Sbjct: 306 RHWGRAIVTGLARVDGWPVAVVASDPYHYGGGWDGPTAEKFIRFVDLAEAFHLPVINMVD 365 Query: 376 ITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFG--AGNYGMCGRAYDPRF 433 I GF +G + E G ++G + + AV A P +VI+ ++G A + GR F Sbjct: 366 IAGFQIGLEAEKAGTMRYGVRALAAVYQATTPWCSVILRRAYGVAAAGHQHMGRF---NF 422 Query: 434 LWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQPILDQYEEQGHPYY 493 + WP+ G + E G+ V K AE G ++ AEI+Q + P+ Sbjct: 423 RYAWPSGNWGSLPIE--GGLEVAYK---AEIEGADDPVQKRAEIEQRV----RSLTSPFR 473 Query: 494 SSARLWDDGVIDPAQTRDVLGLALSASLNAPI-EPS--RFGV 532 S+ + +IDP TR + L A+L AP+ EP +FG+ Sbjct: 474 SAEAFVVEDIIDPRDTRSL--LCEFANLAAPLREPGVRKFGI 513 Lambda K H 0.321 0.137 0.411 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: 722 Number of extensions: 39 Number of successful extensions: 8 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: 535 Length of database: 515 Length adjustment: 35 Effective length of query: 500 Effective length of database: 480 Effective search space: 240000 Effective search space used: 240000 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: 52 (24.6 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