Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_011781995.1 MVAN_RS24365 acetyl/propionyl-CoA carboxylase subunit alpha
Query= reanno::Dino:3607308 (681 letters) >NCBI__GCF_000015305.1:WP_011781995.1 Length = 656 Score = 385 bits (990), Expect = e-111 Identities = 255/699 (36%), Positives = 365/699 (52%), Gaps = 68/699 (9%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 M ++L+ANRGEIA RV T R++GI TVA+Y+DAD A HV AD V + + Y Sbjct: 1 MITRVLVANRGEIARRVFATCRRLGIGTVAVYTDADAGAPHVAEADARVRL---TGTRGY 57 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 + +++ A R +GA+A+HPGYGFLSEN FA A++ G+ +IGPP A+ AMG KI +K Sbjct: 58 LDAAQLIAAARSSGADAIHPGYGFLSENPDFAAAVQDAGLRWIGPPVAAVAAMGSKIEAK 117 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180 K+ A V + D + ++ ++ PV++KASAGGGG+GMR+ + AE Sbjct: 118 KLMAAAGVP--------VLDELDPDTVTADM-LPVLVKASAGGGGRGMRVVRDLAELPAQ 168 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240 ++++ EA ++FGD +F E+++ H+E+QV+AD HG +GERECSIQRR+QK++E Sbjct: 169 VEAARREAQSAFGDPTVFCERYLDAGHHVEVQVMADVHGTVWAVGERECSIQRRHQKIIE 228 Query: 241 EAPSPFLDEAT--RKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHP 298 EAPSP ++ R + E + A A+GY+ AGTVEF+ D F+FLEMNTRLQVEHP Sbjct: 229 EAPSPLVERVAGMRDKLFEAARLAATAIGYSGAGTVEFMADDQGAFFFLEMNTRLQVEHP 288 Query: 299 VTELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRY 358 VTEL +GVDLVE + VA G L + G +IE RLYAEDP N+ P G + + Sbjct: 289 VTELTSGVDLVELQLAVADGATLDPSPP--APRGASIEARLYAEDPANNWQPQPGAVHHF 346 Query: 359 R-PPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRP 417 P V GPL+ G VR D+G+ +G IS++YDPMIAK+ ++ P R Sbjct: 347 DVPTAGVEFGPLDRTG------------VRLDSGITDGAVISVFYDPMIAKVISYAPTRR 394 Query: 418 AAIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAA 477 A + +AL + G+ N + V+ HP F G TAF G + A Sbjct: 395 QAAALLADALTRARIHGVRTNRDLLVNVLRHPAFGDGATDTAFFDTH---GLAELAAPVA 451 Query: 478 DLTRLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWVVTAQDARFDVTIDADPGGSTV 537 D R A +A +A+ R + T+ + + W + A + Sbjct: 452 D-DRTVALSAVAAALADAAHNRSTATVFED---IPSGW----------RNLPAGFQHKSY 497 Query: 538 RFADGTAHRVTSRWTPG-------DSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKV- 589 + G AH V R+T D ++ V +VL V + F + G V V Sbjct: 498 QDHAGRAHDVRYRFTRDGVMIDGHDDVSVVSAGQRQVVLTVSGVDRPFDVTRYGDSVFVD 557 Query: 590 -------HVRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCT 642 V PR P+ LL PMPG V+++ GD V GQ L Sbjct: 558 SPCGCTHFVALPR-------FPDPAAALAHGSLLAPMPGSVLRVGAAPGDTVTAGQPLLW 610 Query: 643 VEAMKMENILRAEKTATVTKINAGAGDSLAVDDVIMEFE 681 +EAMKME+ + A + ++N G + V V+ E Sbjct: 611 LEAMKMEHTITAPTDGVLVELNVEPGRQVEVGAVLARVE 649 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: 1141 Number of extensions: 64 Number of successful extensions: 7 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: 656 Length adjustment: 38 Effective length of query: 643 Effective length of database: 618 Effective search space: 397374 Effective search space used: 397374 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