Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate SM_b20756 SM_b20756 propionyl-CoA carboxylase subunit alpha
Query= reanno::Dino:3607308 (681 letters) >FitnessBrowser__Smeli:SM_b20756 Length = 670 Score = 932 bits (2410), Expect = 0.0 Identities = 472/681 (69%), Positives = 544/681 (79%), Gaps = 14/681 (2%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 MFKKILIANRGEIACRVI+T + +GI TVA+YSDADR+A+HVRMADEAVHIGPSP++QSY Sbjct: 4 MFKKILIANRGEIACRVIRTTKALGIPTVAVYSDADRDAMHVRMADEAVHIGPSPSSQSY 63 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 IVI+ ++ AIR+TGA+AVHPGYGFLSEN FAEALEK+GV FIGPP AIEAMGDKITSK Sbjct: 64 IVIENILAAIRRTGADAVHPGYGFLSENAAFAEALEKDGVTFIGPPVRAIEAMGDKITSK 123 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180 K+A EA V TVPG+MGLI DADEA +I+ EIG+PVMIKASAGGGGKGMRIAWN+ EAREG Sbjct: 124 KLAAEAGVFTVPGHMGLIEDADEAARIAAEIGFPVMIKASAGGGGKGMRIAWNEREAREG 183 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240 FQSS+NEA +SFGDDRIFIEKFVT+PRHIEIQVL D HGN +YLGERECSIQRRNQKV+E Sbjct: 184 FQSSRNEAKSSFGDDRIFIEKFVTEPRHIEIQVLGDKHGNILYLGERECSIQRRNQKVIE 243 Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300 EAPSPFLDE TR+AMGEQ+ ALA+AVGY SAGTVEFIVD RNFYFLEMNTRLQVEHPVT Sbjct: 244 EAPSPFLDEKTRRAMGEQAVALAKAVGYHSAGTVEFIVDAGRNFYFLEMNTRLQVEHPVT 303 Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRP 360 EL+TG+DLVEQMIRVAAG KL Q DV L GWAIE+RLYAEDPYR FLPSIGRLTRYRP Sbjct: 304 ELVTGLDLVEQMIRVAAGAKLAFAQKDVKLDGWAIESRLYAEDPYRTFLPSIGRLTRYRP 363 Query: 361 PVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAI 420 P E +A+G T +RNDTGV+EGGEISMYYDPMIAKLCTWGPDR A+ Sbjct: 364 PEE----GTQADG----------TVIRNDTGVFEGGEISMYYDPMIAKLCTWGPDRLTAV 409 Query: 421 EAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLT 480 AM +ALD FEVEGIGHNLPF+AAVM F +G +TTA+I E++ GF GV L A Sbjct: 410 RAMADALDAFEVEGIGHNLPFLAAVMQQERFHEGRLTTAYIAEEFAGGFHGVALDDASAR 469 Query: 481 RLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWVVTAQDARFDVTIDADPGGSTVRFA 540 +LAA AA + + + R +RISGT+ NH R+VG +WV + VT + G+ VRFA Sbjct: 470 KLAAVAATVNQTLQERASRISGTIGNHRRVVGHEWVTSLDGHEIQVTCEVSADGTYVRFA 529 Query: 541 DGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVRTPRQAELN 600 DGT+ V + W PG + A ID PM +KV+ G R+R+RG DV VR+PR AEL Sbjct: 530 DGTSVSVATDWAPGRTRAAFNIDNQPMSVKVELAGPGIRLRWRGIDVVARVRSPRIAELA 589 Query: 601 DLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRAEKTATV 660 LMP+KLPPDTSKMLLCPMPG+V I V+ G+ V+ GQA+ VEAMKMENILRAEK A V Sbjct: 590 RLMPKKLPPDTSKMLLCPMPGVVTSITVKAGETVEAGQAIAVVEAMKMENILRAEKRAIV 649 Query: 661 TKINAGAGDSLAVDDVIMEFE 681 ++ AG SLAVD++IMEFE Sbjct: 650 KRVAIEAGASLAVDELIMEFE 670 Lambda K H 0.318 0.134 0.392 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: 1282 Number of extensions: 41 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: 681 Length of database: 670 Length adjustment: 39 Effective length of query: 642 Effective length of database: 631 Effective search space: 405102 Effective search space used: 405102 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: 54 (25.4 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