Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_011914338.1 PST_RS16440 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::Smeli:SM_b21124 (662 letters) >NCBI__GCF_000013785.1:WP_011914338.1 Length = 449 Score = 414 bits (1063), Expect = e-120 Identities = 223/451 (49%), Positives = 296/451 (65%), Gaps = 9/451 (1%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 M K+LIANRGEIA R++R + LGI+TVAV+S AD D +HV+LADE++ IG A +A+SY Sbjct: 1 MLEKVLIANRGEIALRVLRACKELGIKTVAVHSTADRDLMHVSLADESVCIGPASSAQSY 60 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L+ I+ AA GA IHPGYGFL+ENADFAE V ++G F+GP IR MG K +AK Sbjct: 61 LSIPAIIAAAEVTGADGIHPGYGFLAENADFAEQVEKSGFTFIGPTADVIRLMGDKVSAK 120 Query: 121 ALMERSGVPVVPGYHGE-EQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGP 179 M+++GVP VPG G +D ARE+GYPV+IKA GGGG+GMR V ++ED Sbjct: 121 DAMKQAGVPTVPGSDGPLPEDEKEALRIAREVGYPVIIKAAGGGGGRGMRVVHKEEDLIA 180 Query: 180 ALEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVI 239 + + R EA +AFG+ V LE++LT PRH+E+QV D GN +HL +RDCSLQRRHQKVI Sbjct: 181 SAKLTRNEAGAAFGNPMVYLEKFLTNPRHVEIQVLADGQGNAIHLGDRDCSLQRRHQKVI 240 Query: 240 EEAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQ 299 EEAPAP + E RR + V+A IGY GAGT EF+ + N FYF+EMNTR+Q Sbjct: 241 EEAPAPLIDEEARRKVQARCVKACIDIGYRGAGTFEFLYEDGN------FYFIEMNTRVQ 294 Query: 300 VEHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGR 359 VEHPVTE +TGID+V+ L + G+ L KQ D+ + G A E R+ AEDP R F+P+ G+ Sbjct: 295 VEHPVTEMVTGIDIVKEMLLIGGGQKLSIKQEDVVIRGHAVECRINAEDP-RTFMPSPGK 353 Query: 360 LTELSFPEGTS-RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGG 418 + P G RVDS + G ++ P+YD LI KLI G NR A+GR+++AL E + G Sbjct: 354 VKHFHAPGGNGVRVDSHLYDGYSVPPHYDSLIGKLITFGANRDEAMGRMRNALDELIVDG 413 Query: 419 TVTNRDFLIRLTEEHDFRSGHPDTGLIDREI 449 TN L + F G + +++++ Sbjct: 414 IKTNAPLHRDLVRDPGFCKGGVNIHYLEKKL 444 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: 810 Number of extensions: 36 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: 449 Length adjustment: 35 Effective length of query: 627 Effective length of database: 414 Effective search space: 259578 Effective search space used: 259578 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: 52 (24.6 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