Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate HSERO_RS01925 HSERO_RS01925 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::pseudo5_N2C3_1:AO356_01595 (649 letters) >FitnessBrowser__HerbieS:HSERO_RS01925 Length = 459 Score = 398 bits (1022), Expect = e-115 Identities = 211/429 (49%), Positives = 281/429 (65%), Gaps = 4/429 (0%) Query: 9 LLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 +L+ANRGEIA R+ R R +G+ TV VHS DR+A++ + AD V +G + + SYL + Sbjct: 5 ILIANRGEIALRIQRACRELGIKTVVVHSEADREAKYVKLADESVCIGPAPSTLSYLNMP 64 Query: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKTLME 128 +I+AA+ + AQAIHPGYGFLSENA FA +E +G +F+GP A I MG K +AK M Sbjct: 65 AIISAAEVTDAQAIHPGYGFLSENADFAERVEKSGFVFIGPRAENIRMMGDKVSAKQAMI 124 Query: 129 TAGVPLVPGYHGEAQDL-ETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187 AGVP VPG G D + A +IGYPV++KA GGGG+GM+VV + L A+ Sbjct: 125 RAGVPCVPGSDGALPDNPKEIVQIARKIGYPVIIKAAGGGGGRGMRVVHTEAALINAVTM 184 Query: 188 AQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247 + EA ++FG+ + +EKYL PRHVEIQ+ AD+H ++L ERDCS+QRRHQKV+EEAP Sbjct: 185 TKTEAGAAFGNPEVYMEKYLENPRHVEIQILADEHKQAIWLGERDCSMQRRHQKVIEEAP 244 Query: 248 APGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAI 307 APG+ ++ +GE A + + Y GAGT EFL + EF+F+EMNTR+QVEHPVTE I Sbjct: 245 APGIPRKIIEKIGERCAEACRKMNYRGAGTFEFLYE-NEEFYFIEMNTRVQVEHPVTEMI 303 Query: 308 TGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPGNDFLPATGRLALYRESAE 367 TG+D+V QIR+A GE L Q + L GHAIE R+ AEDP F+P+ GR+ + Sbjct: 304 TGVDIVQEQIRIAAGEKLRYRQRDIELKGHAIECRINAEDPFK-FIPSPGRITAWHVPG- 361 Query: 368 GPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGLKTNIGFL 427 GPG RVDS G + P YD M+GK+IA+G REQA R+ L E V+ G+ TNI Sbjct: 362 GPGIRVDSHAYSGYFVPPNYDSMVGKVIAYGATREQAIRRMQIALSEMVVEGISTNIPLH 421 Query: 428 RRIVAHPAF 436 R ++ F Sbjct: 422 RELMVDARF 430 Lambda K H 0.319 0.134 0.390 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: 713 Number of extensions: 31 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: 649 Length of database: 459 Length adjustment: 35 Effective length of query: 614 Effective length of database: 424 Effective search space: 260336 Effective search space used: 260336 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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