Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_036256001.1 METAC_RS0105105 3-methylcrotonyl-CoA carboxylase
Query= reanno::Dino:3607308 (681 letters) >NCBI__GCF_000427445.1:WP_036256001.1 Length = 684 Score = 494 bits (1271), Expect = e-144 Identities = 293/702 (41%), Positives = 397/702 (56%), Gaps = 52/702 (7%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 +F KILIANRGEIACR+IKTAR++ I TV +YSDADR ALHV +ADEA+ IGP+PA +SY Sbjct: 4 LFSKILIANRGEIACRIIKTARRLAISTVGVYSDADREALHVALADEALRIGPAPARESY 63 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 + K++ A GAEAVHPGYGFL+EN FAEA + G+ FIGPP +AI AMGDK +K Sbjct: 64 LEGVKIIAAALAAGAEAVHPGYGFLAENAAFAEACAEAGLVFIGPPPDAIRAMGDKAEAK 123 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGE----IGYPVMIKASAGGGGKGMRIAWNDAE 176 + + A+V +PGY G D+ ++ GE IGYPVMIK SAGGGGKGM+I A Sbjct: 124 ALMERASVPLLPGYHG----PDQGLRRLGEAADAIGYPVMIKPSAGGGGKGMKIVAEAAA 179 Query: 177 AREGFQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQ 236 +S++ EAA++FGDDR+ +EKF+ PRH+E+Q+ AD N ++L +R+CSIQRR+Q Sbjct: 180 FAAAVESARREAASAFGDDRLLVEKFLPAPRHVEVQIFADARQNYVHLFDRDCSIQRRHQ 239 Query: 237 KVVEEAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRN-FYFLEMNTRLQV 295 K++EEAP+P L + R+ M E + A A+A+ Y AGT+EF+V + FYF+EMNTRLQV Sbjct: 240 KIIEEAPAPGLSDDLRRHMREAALAAAKAISYVGAGTIEFLVPASLDAFYFMEMNTRLQV 299 Query: 296 EHPVTELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRL 355 EHP TE+I G+DLVE IR+AAGE LP+ Q + G AIE RLYAEDP R+FLP GR+ Sbjct: 300 EHPATEMIAGLDLVEWQIRIAAGEALPLEQAQILSHGHAIEARLYAEDPMRDFLPQPGRI 359 Query: 356 TRYRPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPD 415 R D P+ +R D GV GE+ +YYDP+IAKL WG D Sbjct: 360 ERL-------------------DLPTPSPQLRIDAGVAAPGEVPIYYDPLIAKLIVWGAD 400 Query: 416 RPAAIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLG 475 RPAAI +R ALD +EG+ N+ + + H + + T FI D Sbjct: 401 RPAAIRRLRAALDDVFIEGVATNIELLRRIAGHQAYADAALDTGFIARHSADLLAPPGPP 460 Query: 476 AADLTRLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTD-WVVTA--QDARFDVTIDADP 532 + ++ +AA +R E R + + D D W++ ++ IDA P Sbjct: 461 SREILAMAAVGLLCWR-EEAARAQAKRSRDQWSPWSSRDGWLLNGRLRETLRLREIDAAP 519 Query: 533 ------GGSTVRFA-------DGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFR 579 G + +R DG P D V++DG +GF Sbjct: 520 RDEIAIGVAYLRRGWRLDLPQDGMVLYARGALAP-DGALCVDLDGHQRSASWTGCPAGFA 578 Query: 580 MRFRGADVKVHVRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQA 639 + +G V+ A ++ E P L+ PMPG + + VE G V+ Q Sbjct: 579 VFRKGEAVR------HFALIDGTGEEASKPQARGRLVSPMPGRIAALLVEPGARVEANQP 632 Query: 640 LCTVEAMKMENILRAEKTATVTKINAGAGDSLAVDDVIMEFE 681 + +EAMKME+ LRA +T+ AGD A + FE Sbjct: 633 ILVLEAMKMEHQLRAPGDGLITEFYVRAGDQAAEGAELARFE 674 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: 1271 Number of extensions: 56 Number of successful extensions: 6 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: 684 Length adjustment: 39 Effective length of query: 642 Effective length of database: 645 Effective search space: 414090 Effective search space used: 414090 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