Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate HSERO_RS20550 HSERO_RS20550 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__HerbieS:HSERO_RS20550 Length = 462 Score = 421 bits (1082), Expect = e-122 Identities = 233/444 (52%), Positives = 295/444 (66%), Gaps = 6/444 (1%) Query: 4 KLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESYLAS 63 KLLIANRGEIA RIIR A+ LGI TVA SDAD D+L +ADE RIG A A SYL Sbjct: 7 KLLIANRGEIAVRIIRAAQALGITTVAACSDADTDSLAARMADEVQRIGPARADRSYLNV 66 Query: 64 APIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAKALM 123 +++AAR GA A+HPGYGFLSENA FAEAV AG+IFVGP IR MG K A+ Sbjct: 67 DALLKAARDSGADALHPGYGFLSENAAFAEAVNAAGLIFVGPQADTIRRMGDKAEARRTA 126 Query: 124 ERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPALEA 183 +GVPVVPG GE +D + A EIGYP+LIKA AGGGG+G+R + Sbjct: 127 AAAGVPVVPGSAGELEDLATALACADEIGYPLLIKASAGGGGRGIRMARDATELAREFPL 186 Query: 184 ARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIEEAP 243 A+ EA++AFG +V LER++ + RHIE+Q+ GD VHLFER+CSLQRR QKV+EEAP Sbjct: 187 AQAEAQAAFGSAAVYLERFIRRARHIEVQILGDGE-RAVHLFERECSLQRRRQKVLEEAP 245 Query: 244 APGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQVEHP 303 +P +T R+A+ D+AVR A+ + Y GAGT+E++ D +G F+F+EMNTR+QVEHP Sbjct: 246 SPALTPAQRQALCDSAVRLAERLHYRGAGTLEYLFDDESG----EFFFIEMNTRIQVEHP 301 Query: 304 VTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRLTEL 363 VTE ITGIDLV+ LR+A GEPL +Q+DI M G A E R+ AEDP R F P G + EL Sbjct: 302 VTEMITGIDLVQAMLRIAGGEPLGLQQSDIRMQGAALEMRINAEDPERNFFPCPGTVAEL 361 Query: 364 SFPEGTS-RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGTVTN 422 +P+G RV+S + G I PYYD L+AKL+VHG++R+ A+ R Q A+ RI G T Sbjct: 362 QWPQGEGIRVESHLYAGYRIPPYYDSLLAKLVVHGKDRAQAIARAQAAVLATRITGMATT 421 Query: 423 RDFLIRLTEEHDFRSGHPDTGLID 446 L + +S DTG ++ Sbjct: 422 LSLHQWLLADARVQSARFDTGALE 445 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: 761 Number of extensions: 32 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: 662 Length of database: 462 Length adjustment: 36 Effective length of query: 626 Effective length of database: 426 Effective search space: 266676 Effective search space used: 266676 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