Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_046007990.1 OLEAN_RS02940 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::Dino:3607308 (681 letters) >NCBI__GCF_000967895.1:WP_046007990.1 Length = 678 Score = 483 bits (1244), Expect = e-141 Identities = 291/683 (42%), Positives = 409/683 (59%), Gaps = 43/683 (6%) Query: 2 FKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYI 61 F K+L+ANRGEIA RVI++A+ +G +TVA++S+AD NA HV +ADEA+ IG S +SY+ Sbjct: 11 FTKVLVANRGEIAVRVIRSAQSLGYRTVAVFSEADANAPHVSIADEAICIGASAVGESYL 70 Query: 62 VIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKK 121 V +K++ A ++TGA+A+HPGYGFLSEN FA+A + FIGP +AI+ MG K SK Sbjct: 71 VAEKLIAAAKKTGADAIHPGYGFLSENSAFAKACVDADIVFIGPRPDAIDLMGSKRHSKI 130 Query: 122 IAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGF 181 A V +PGY G D + EIG PVM+KASAGGGG+GMR+ + + E Sbjct: 131 AMIAAGVPCIPGYEGADQSDDALRNAAIEIGMPVMLKASAGGGGRGMRLVTDANDLDELI 190 Query: 182 QSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEE 241 +S+++EA N+FG+ + IEK V QPRHIEIQV AD+ GN +YLGER+CS+QRR+QKVVEE Sbjct: 191 KSARSEALNAFGNGELIIEKAVMQPRHIEIQVFADSFGNTVYLGERDCSVQRRHQKVVEE 250 Query: 242 APSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVTE 301 APSPF++ A RK+MGE + A++ Y AGTVEF+ D D NFYFLEMNTRLQVEHPVTE Sbjct: 251 APSPFVNPAMRKSMGEAAVNAAKSCNYVGAGTVEFLADSDGNFYFLEMNTRLQVEHPVTE 310 Query: 302 LITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRPP 361 LITG+DLV +RVAAG+KL ++Q+DVTLTG A+E RLYAEDP NF+P G L ++P Sbjct: 311 LITGLDLVAMQLRVAAGDKLSISQEDVTLTGHAMEVRLYAEDPGANFIPQTGLLNLWQP- 369 Query: 362 VEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAIE 421 A+G VR D+G+ +G IS +YDPM+AK+ +G +R A Sbjct: 370 ---ASG----------------DGVRIDSGIQQGQTISSFYDPMLAKIIAYGENREEARR 410 Query: 422 AMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLTR 481 + A++ ++ GI N F+A+++ + FI+GE TTAFI + + L Sbjct: 411 RLVCAVEDSKLLGIKDNRAFLASILCNDTFIQGEATTAFIGDDFSQD--------PSLQP 462 Query: 482 LAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWV-VTAQDARFDVTIDADPGGSTVRFA 540 LAA + A I SG+ G+ + ++ +D F++ + A TV F Sbjct: 463 LAAQYREVALAASILSAIQSGSSGWQNNRTGSRIIKLSCEDQTFELALTAIENTITVDFV 522 Query: 541 DGTAHRVTSRWTPGDSLATVE-IDGAPMVLKV---DKITSGFRMRFRGAD-----VKVHV 591 A T++ + T++ I+ + +LK D + + + +G +VH+ Sbjct: 523 TEAAD--TNKESQAKEKQTIKIIEQSEDILKYVQDDVVRTVTYSQTKGVGDALGCNQVHL 580 Query: 592 RTP-RQAELND--LMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKM 648 D L K S +L M G +V + V+VGD V GQ L +EAMKM Sbjct: 581 AASYGNLTFTDISLQSAKKNKGGSDQVLASMDGGMVDVMVKVGDVVNVGQTLAVLEAMKM 640 Query: 649 ENILRAEKTATVTKINAGAGDSL 671 E+ L+A T+ ++ AGD + Sbjct: 641 EHPLKAGVAGTIAEVLIKAGDQV 663 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: 1110 Number of extensions: 37 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 681 Length of database: 678 Length adjustment: 39 Effective length of query: 642 Effective length of database: 639 Effective search space: 410238 Effective search space used: 410238 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