Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate HSERO_RS23460 HSERO_RS23460 3-methylcrotonyl-CoA carboxylase subunit alpha
Query= SwissProt::Q5LUF3 (681 letters) >FitnessBrowser__HerbieS:HSERO_RS23460 Length = 671 Score = 525 bits (1351), Expect = e-153 Identities = 307/695 (44%), Positives = 415/695 (59%), Gaps = 40/695 (5%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF KILIANRGEIACRV TAR++GI+TVA+YSDAD +A HV DE+V +GP PA +SY Sbjct: 1 MFTKILIANRGEIACRVAATARRLGIATVAVYSDADARAKHVAACDESVRLGPAPARESY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 + +K++AA ATGAQA+HPGYGFLSEN+ FA+A G++F+GPP AIEAMG K +K Sbjct: 61 LCAEKIIAAALATGAQAIHPGYGFLSENAGFAQACAQAGLVFIGPPASAIEAMGSKAAAK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 + ++A V VPGY G +++ +++IGYPV++KASAGGGGKGMR+ ++ Sbjct: 121 ALMEQAAVPLVPGYHGEEQESGLLHSQADRIGYPVLLKASAGGGGKGMRVVERSEDFDAA 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 S K EA SFGDDR+ +EK++T+PRHIEIQV D HG+ +YL ER+CS+QRR+QKV+E Sbjct: 181 LASCKREAIASFGDDRVLVEKYLTRPRHIEIQVFADGHGHCVYLFERDCSVQRRHQKVLE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAP+P + E R AMGE AVA A+AVGY AGTVEFI + +FYF+EMNTRLQVEHPVT Sbjct: 241 EAPAPGMSEERRAAMGEAAVAAARAVGYVGAGTVEFIANQDGSFYFMEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 E+ITG+DLVE +RVAAG+ L + Q +++ G AIE R+YAE+P +GFLP+IG LTR R Sbjct: 301 EMITGLDLVEWQLRVAAGQALPLKQEQLRIHGHAIEARIYAENPEKGFLPAIGTLTRMRS 360 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 A V + AP A VR D GV EG IS +YDPMIAKL W P R AA+ Sbjct: 361 AA-------AVEFRLGQSAPGDPAHVRIDAGVREGDAISPFYDPMIAKLIVWGPDRDAAL 413 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 M+ AL ++V G+ N+ FL ++ F + + T I F + P+T+ Sbjct: 414 RNMQRALAQYQVVGLATNIAFLQRLVAGQAFSTAALDTGLIERHRDTLFPPPSSPDTETL 473 Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGSTVSFD 540 +A AA A+ R+ D +R G W + + T+ +HD + Sbjct: 474 ALAIAAILQQEHAQAERS------DPWSQRNG--WRLNTR---LLRTLRFEHDAGDTT-- 520 Query: 541 DGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRI-----RTRGADLK-----VH 590 V D+ Q +L+ +G L++ G I RT AD+ +H Sbjct: 521 ------VQLDYAGDGQHWSLLTNGQTHALQLHAADGDTLIISLDGRTLRADVLREGEWLH 574 Query: 591 VRTPRQAELARLMPEKLPPDTSK----MLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAM 646 V R + S+ L PMPG IV + V+ G V G L +EAM Sbjct: 575 VFDAHGQHSLRHVDPLAHAGHSEAEGGRLTAPMPGKIVALLVQKGASVAHGTPLLIMEAM 634 Query: 647 KMENILRAEKKGVVAKINASAGNSLAVDDVIMEFE 681 KME+ + A GVV + + G+ +A ++EF+ Sbjct: 635 KMEHTIAAPADGVVEDLLYAVGDQVAEGAQLLEFK 669 Lambda K H 0.317 0.134 0.387 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: 1115 Number of extensions: 48 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: 671 Length adjustment: 39 Effective length of query: 642 Effective length of database: 632 Effective search space: 405744 Effective search space used: 405744 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