Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate CA265_RS02215 CA265_RS02215 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__Pedo557:CA265_RS02215 Length = 503 Score = 476 bits (1226), Expect = e-139 Identities = 254/467 (54%), Positives = 324/467 (69%), Gaps = 6/467 (1%) Query: 3 SKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESYLA 62 SKLL+ANRGEIA RI+R+A+ +GI+TVAV+S+AD +ALHV ADEA+ IG AP+ +SYL Sbjct: 12 SKLLVANRGEIALRIMRSAKEMGIKTVAVFSEADRNALHVRYADEAVCIGPAPSNQSYLV 71 Query: 63 SAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAKAL 122 I+ A + GA+AIHPGYGFLSENA FA+ VA+AG+I VGP P A+ MG K +AKA Sbjct: 72 GEKIIGACKLTGAEAIHPGYGFLSENAGFAQMVADAGLILVGPSPQAMETMGNKLSAKAA 131 Query: 123 MERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPALE 182 + +P+VPG QD + RA E+G+P+LIKA AGGGGKGMR VER EDF ++ Sbjct: 132 ALKYNIPMVPGTEEAIQDVNEAKQRAIEVGFPILIKAAAGGGGKGMRIVERAEDFEEQMQ 191 Query: 183 AARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIEEA 242 A EA SAFGDG+V +ERY+T PRHIE+QV GD HGNIVHLFER+CS+QRRHQKVIEEA Sbjct: 192 LAVSEATSAFGDGAVFIERYVTSPRHIEIQVLGDNHGNIVHLFERECSVQRRHQKVIEEA 251 Query: 243 PAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQVEH 302 P+ +T E+R+ MG AV A+++ Y GAGTVEFI D F+F+EMNTRLQVEH Sbjct: 252 PSSVLTEEIRQRMGKCAVDVARSVNYTGAGTVEFILDENL-----DFFFLEMNTRLQVEH 306 Query: 303 PVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRLTE 362 PVTE ITGIDLV+ QL++ASGE L Q D+ ++G A E R+YAEDPA FLP G L Sbjct: 307 PVTELITGIDLVKEQLKIASGEKLSFSQEDLKISGHAVELRVYAEDPANNFLPDIGTLQT 366 Query: 363 LSFPEGTS-RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGTVT 421 + P+G RVD G QG I YYDP+IAKLI +G++R A+ R+ A++E I G T Sbjct: 367 YNTPKGNGVRVDDGFEQGMEIPIYYDPMIAKLITYGKDREEAIERMVRAIEEYDITGIET 426 Query: 422 NRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPVAPGDEALALAAI 468 F + + F++G+ DT + + + + V EAL A I Sbjct: 427 TLGFGKFVMQHEAFKTGNFDTHFVGKYFKPESLKVQDETEALIAAVI 473 Lambda K H 0.319 0.135 0.394 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: 740 Number of extensions: 31 Number of successful extensions: 3 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: 662 Length of database: 503 Length adjustment: 36 Effective length of query: 626 Effective length of database: 467 Effective search space: 292342 Effective search space used: 292342 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 (21.8 bits) S2: 53 (25.0 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