Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate 6937189 Sama_1359 3-methylcrotonyl-CoA carboxylase alpha subunit (RefSeq)
Query= metacyc::MONOMER-13589 (666 letters) >FitnessBrowser__SB2B:6937189 Length = 673 Score = 505 bits (1301), Expect = e-147 Identities = 292/678 (43%), Positives = 405/678 (59%), Gaps = 30/678 (4%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MF K+LIANRGEIACRVI+TAR MGI+TVAVYSDADR+A HV++ADE+ ++G SY Sbjct: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + + I++ K GAEA+HPGYGFLSE FA A EA+G+ F+GP S AI+AMG K +K Sbjct: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 + ++AGV VPGY G + + +IGYP++IKA+ GGGGKGMRI SE+E+K Sbjct: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 +S++ EAA+SFG+D++ +E+++ QPRH+E+QV AD GNCVYL +R+CSIQRR+QKV+E Sbjct: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAP+P L ++ RK MGE A A AKA+ Y AGTVEF++D +F+F+EMNTRLQVEHPVT Sbjct: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300 Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360 E++TG DLV+ + VAAG +LP +Q +++I+G A E R+YAEDP FLP+ G+LT R Sbjct: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360 Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420 P P+ VR D+GV E IS YYDPMIAKL W +R A+ + AL + V G+ Sbjct: 361 P----EPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGL 416 Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480 HN+ F+ + +HP F + + +T FI Y D G DE V A + Sbjct: 417 KHNIEFLSNIAEHPAFAQANFSTDFIG-RYGDALIGDSRDEADTAFVLAVLTQLR----- 470 Query: 481 RRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSDWTPGQ 540 R +S + H+ W +L+G +++ R S D R +++ T Sbjct: 471 LREAVSQDVAGHDPF--SPW-SSLKG----FRLSSPRRHSVTLLDDAHQSR-SAELTESN 522 Query: 541 PLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALL----------MPE 590 L ++ + + + + + G +KV V L + + Sbjct: 523 GRYQLCLNDKLIELSGSIEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYHFREVLGQ 582 Query: 591 KLPPDTSK--YLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKI 648 L S L PM G VV VA GD+V GQ L +EAMKME + A G V + Sbjct: 583 VLEETASSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEF 642 Query: 649 AAAPGASLRVDDVIMEFE 666 APG + +++ E Sbjct: 643 FFAPGELVSDGTLLLALE 660 Lambda K H 0.318 0.134 0.386 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: 1042 Number of extensions: 55 Number of successful extensions: 4 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: 666 Length of database: 673 Length adjustment: 39 Effective length of query: 627 Effective length of database: 634 Effective search space: 397518 Effective search space used: 397518 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 Apr 09 2024. 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