Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_050656086.1 C1M55_RS09265 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::Dino:3607308 (681 letters) >NCBI__GCF_002893965.1:WP_050656086.1 Length = 679 Score = 501 bits (1291), Expect = e-146 Identities = 302/683 (44%), Positives = 406/683 (59%), Gaps = 48/683 (7%) Query: 5 ILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYIVID 64 +L+ANRGEIA RVI+T R++GI++VA+YSDAD NA HVR AD AV+IGP+ A +SY+VID Sbjct: 10 VLVANRGEIAVRVIRTLRELGIRSVAVYSDADANARHVREADTAVNIGPAAARESYLVID 69 Query: 65 KVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKKIAQ 124 KV+DA + TGA+ +HPGYGFLSEN F+ A G+AF+GP +AIE MGDKIT+K Sbjct: 70 KVIDAAKSTGAQGIHPGYGFLSENSAFSAACAAAGIAFLGPSEHAIEVMGDKITAKNSVA 129 Query: 125 EANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGFQSS 184 +V VPG +E + + +IGYPV++K SAGGGGKGMR+ + A E +S+ Sbjct: 130 AFDVPVVPGIARPNLTDEELIAAAEDIGYPVLVKPSAGGGGKGMRLVEDPANLAEALRSA 189 Query: 185 KNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEEAPS 244 + EAA+SFGDD +F+E+FV +PRHIE+QVLAD HGN ++LGERECS+QRR+QKV+EEAPS Sbjct: 190 RREAASSFGDDTLFLERFVLRPRHIEVQVLADQHGNVVHLGERECSLQRRHQKVIEEAPS 249 Query: 245 PFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDR--NFYFLEMNTRLQVEHPVTEL 302 P LD+ TR +G +C A++V Y AGTVEFIV D+ F+F+EMNTRLQVEHPVTE+ Sbjct: 250 PLLDQVTRDRIGAAACNTARSVDYTGAGTVEFIVSADKPDEFFFMEMNTRLQVEHPVTEM 309 Query: 303 ITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRPPV 362 +TG+DLVE +RVAAGEKL +Q D+TLTG AIE R+YAEDP R FLP+ GR+ V Sbjct: 310 VTGLDLVEWQVRVAAGEKLAFSQSDITLTGHAIEARVYAEDPGRGFLPTGGRV------V 363 Query: 363 EVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAIEA 422 ++ PSG + VR D+G+ G + YDPM++K+ PDR A+ Sbjct: 364 DLV-------------EPSG-SGVRVDSGLLAGTVVGSDYDPMLSKVIAHAPDRAGALRK 409 Query: 423 MRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLTRL 482 + AL V G+ N+ F ++ P I G + T + + D AAD + Sbjct: 410 LDRALGDTAVLGVVTNIEFARFLLADPDVIAGNLDTGLLDRRVED------FVAADASDE 463 Query: 483 AAAAAAMFRVAEIRRTRISGTLDNHERMVG--------TDWVVTAQDARFDVTIDADPGG 534 AAA +R + R S D + G T ++A V I P Sbjct: 464 VLIAAAAYR--WLSRWTTSERFDPWDVPSGWRVGTPAPTSIRLSAGTRTAHVAIVGVPAA 521 Query: 535 STVRFADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVRTP 594 + V +G+ R S G LA V IDG V + G + G HVR Sbjct: 522 AKVE-VEGSQPRAFSATLTGSELAVV-IDGRRRTFVVAETDGGLWLAGGGT---WHVR-- 574 Query: 595 RQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRA 654 AE++ +K D + PMPG V+ ++VE G V GQ L VEAMKME+ L + Sbjct: 575 EVAEVSVRGEDKHAGDAE--IASPMPGAVIAVNVENGAAVSAGQPLVVVEAMKMEHSLTS 632 Query: 655 EKTATVTKINAGAGDSLAVDDVI 677 + ++ GD + VD V+ Sbjct: 633 PIDG-IVEVLVRQGDQVMVDQVL 654 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: 1146 Number of extensions: 51 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: 681 Length of database: 679 Length adjustment: 39 Effective length of query: 642 Effective length of database: 640 Effective search space: 410880 Effective search space used: 410880 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 24 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