Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_045585974.1 AL072_RS28295 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= SwissProt::Q5LUF3 (681 letters) >NCBI__GCF_001305595.1:WP_045585974.1 Length = 667 Score = 541 bits (1393), Expect = e-158 Identities = 319/693 (46%), Positives = 418/693 (60%), Gaps = 44/693 (6%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF+KILIANRGEIACRVI+TAR+MGI TVA++S+AD A+HVQMADEAV IGP P +SY Sbjct: 1 MFDKILIANRGEIACRVIRTARRMGIRTVAVHSEADAHAMHVQMADEAVCIGPAPVGESY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 + D ++ R TGAQA+HPGYGFLSEN+ FA A A GV+F+GPP AI MG K SK Sbjct: 61 LRGDVILDVARRTGAQAIHPGYGFLSENAGFAAACAAAGVVFIGPPIDAIRVMGSKAESK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 ++ A+V VPGY G +D + +IGYPV++KASAGGGGKGMR+ E + Sbjct: 121 RLMANADVPLVPGYHGTDQDFATLSAEAERIGYPVLVKASAGGGGKGMRVVRAAAELADA 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 ++ EA +FGDD + +EK++++PRH+EIQV CD+HGNG+YL ER+CS+QRR+QKV+E Sbjct: 181 VAGAQREAKAAFGDDSLLLEKYLSRPRHVEIQVFCDTHGNGVYLFERDCSVQRRHQKVIE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAP+P L + RR MGE AVA AKAV Y AGTVEF+ + FYF+EMNTRLQVEHPVT Sbjct: 241 EAPAPNLPDDLRRRMGEAAVAAAKAVSYVGAGTVEFLYE-DGGFYFIEMNTRLQVEHPVT 299 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 E ITG+DLVE +RVA+G L + Q + G A E RLYAEDP R FLP+IGRL R RP Sbjct: 300 EKITGLDLVEWQLRVASGAELPLRQDQLTRRGHAFEARLYAEDPQRDFLPAIGRLLRLRP 359 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 PAET VR DTGV EG ++MYYDPMIAKL W R +A+ Sbjct: 360 PAET-------------------EHVRVDTGVREGDSVTMYYDPMIAKLIVWDEDRDSAL 400 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 +R+AL +EV G+ N+ FL A+ HP F + ++ T FI E + P D Sbjct: 401 RRLRVALAEYEVVGVTTNVAFLGAIAGHPAFRAVEIDTGFI-ERHRADLLPPPAPVADRA 459 Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHER-------RVGTEWVVTLQGAD----FPVTIA 529 AA+ + + + E + + R D H R+ E L+ D VT+ Sbjct: 460 LAAASLSVLLKRREEAQAALRARSDRHSPWLLANGWRLNEENHYDLRLMDGETAREVTLH 519 Query: 530 ADHDGSTVSFDDGSSMRVTS-DWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLK 588 D V+ D G M VT T G A L DG V + + GA + Sbjct: 520 FRGDDYEVAVDGGKPMPVTGVSLTDGVLTATL--DGMRTRATVVRQGLDLTVLIDGAVSR 577 Query: 589 VHVRTPRQAELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKM 648 + + P AR ++ S L PMPG +V+V VE GQ V+ G L +EAMKM Sbjct: 578 LTLDDPS----ARAAEQE---GGSGRLTAPMPGTVVRVLVEPGQSVEAGTPLMLLEAMKM 630 Query: 649 ENILRAEKKGVVAKINASAGNSLA--VDDVIME 679 E+ ++A G V+ +N SAG+ ++ VD ++++ Sbjct: 631 EHTIKAPAAGTVSAVNFSAGDQVSEGVDLLVLD 663 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: 1162 Number of extensions: 51 Number of successful extensions: 4 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: 667 Length adjustment: 39 Effective length of query: 642 Effective length of database: 628 Effective search space: 403176 Effective search space used: 403176 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