Align propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized)
to candidate AO353_20335 AO353_20335 3-methylcrotonyl-CoA carboxylase
Query= BRENDA::P05165 (728 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20335 Length = 649 Score = 493 bits (1268), Expect = e-143 Identities = 284/671 (42%), Positives = 396/671 (59%), Gaps = 38/671 (5%) Query: 66 ILVANRGEIACRVIRTCKKMGIKTVAIHSDVDASSVHVKMADEAVCVGPAPTSKSYLNMD 125 +LVANRGEIACRV+RT K +G+ TVA+HS D + H + AD V +G + + SYL +D Sbjct: 9 LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 Query: 126 AIMEAIKKTRAQAVHPGYGFLSENKEFARCLAAEDVVFIGPDTHAIQAMGDKIESKLLAK 185 ++ A K + AQA+HPGYGFLSEN FAR + A ++F+GP AI AMG K +K L + Sbjct: 69 KLLAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 128 Query: 186 KAEVNTIPGFDGVVKDAEEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRLS 245 A V +PG+ G +D E A IGYPV++KA+AGGGGKGM++ D + + + Sbjct: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188 Query: 246 SQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEEAPS 305 +EA SSFGD R+L+EK++ PRH+EIQV D+HGN L+LNER+CSIQRR+QKVVEEAP+ Sbjct: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248 Query: 306 IFLDAETRRAMGEQAVALARAVKYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPVTECIT 365 L A+ R+AMGE AV A+A+ Y AGTVEFL+DS+ F+F+EMNTRLQVEHPVTE IT Sbjct: 249 PGLSAQLRKAMGEAAVRAAQAIGYVGAGTVEFLLDSRGEFFFMEMNTRLQVEHPVTEAIT 308 Query: 366 GLDLVQEMIRVAKGYPLRHKQADIRINGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPLH 425 GLDLV IRVA+G PL QA + + G A+E R+YAEDP F LP+ G L+ Y+E Sbjct: 309 GLDLVAWQIRVAQGEPLPMTQAQVPLLGHAIEVRLYAEDPSNDF-LPATGHLALYRESAA 367 Query: 426 LPGVRVDSGIQPGSDISIYYDPMISKLITYGSDRTEALKRMADALDNYVIRGVTHNIALL 485 PG RVDSG++ G IS +YDPM+ KLI +G DR +A R+ L+ + I G+ NI L Sbjct: 368 GPGRRVDSGVEEGDSISPFYDPMLGKLIAWGVDREQARLRLLSMLEEFAIGGLKTNINFL 427 Query: 486 REVIINSRFVKGDISTKFLSDVYPDGFKGHMLTKSEKNQLLAIASSLFVAF-QLRAQHFQ 544 R +I + F ++ T F+ ++QLL + L AF Q AQ F Sbjct: 428 RRIIGHPAFAAAELDTGFI--------------PRYQDQLLPAPNELSDAFWQAAAQAFA 473 Query: 545 ENSRMPVIKPDI-------ANWELSVKLHDKVHTVVASNNGSVFSVEVDGSKLNVTSTWN 597 ++ V D + + + +H + ++ + T Sbjct: 474 QSQAHHVRADDPGSPWAVGSGFRAGLPAETTLHLSCEDQDRAITLATAE------TRNTE 527 Query: 598 LASPLLSVSVDGTQRTVQCLSREAGGNMSIQFLGTVYKVNILTRLAAELNKFMLEKVTED 657 L L V G +R + + + + +Q+ G + + + +AA + + Sbjct: 528 LNGEQLLVEHHGLRRQHRAIRQ--AETLYLQWEGELRCIKLYDPIAA-------VEASHS 578 Query: 658 TSSVLRSPMPGVVVAVSVKPGDAVAEGQEICVIEAMKMQNSMTAGKTGTVKSVHCQAGDT 717 L +PM G +V V V PG V G ++ V+EAMKM++S+ A G VK+++CQ G+ Sbjct: 579 HQGGLTAPMNGSIVRVLVTPGQTVETGAQLVVLEAMKMEHSIRAPHAGVVKALYCQEGEM 638 Query: 718 VGEGDLLVELE 728 V EG LVELE Sbjct: 639 VNEGSALVELE 649 Lambda K H 0.318 0.134 0.385 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: 1016 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 728 Length of database: 649 Length adjustment: 39 Effective length of query: 689 Effective length of database: 610 Effective search space: 420290 Effective search space used: 420290 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