Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF4012 Psest_4085 Biotin carboxylase
Query= reanno::Smeli:SM_b21124 (662 letters) >FitnessBrowser__psRCH2:GFF4012 Length = 471 Score = 411 bits (1056), Expect = e-119 Identities = 228/476 (47%), Positives = 291/476 (61%), Gaps = 10/476 (2%) Query: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 M KLLIANRGEIA RI+R +G+R+VAV+S+AD ALHV ADEA IG P A Y Sbjct: 1 MIKKLLIANRGEIAVRIVRACAEMGVRSVAVFSEADRHALHVKRADEAHFIGEDPLA-GY 59 Query: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 L +V A G A+HPGYGFLSENA+ A+ AE G+ FVGP IR MG K A+ Sbjct: 60 LNPRKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFVGPSAEVIRRMGDKTEAR 119 Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 M ++GVPV PG G +D + A IGYPV++KA +GGGG+G+RR Q + A Sbjct: 120 RSMIKAGVPVTPGTEGNVRDLAEALREAERIGYPVMLKATSGGGGRGIRRCNSQAELESA 179 Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 EA AFG V LE+ + +P+HIE Q+ D GN VHLFERDCS+QRR+QK+IE Sbjct: 180 YPRVISEATKAFGSAEVFLEKCIVEPKHIEAQILADSFGNTVHLFERDCSIQRRNQKLIE 239 Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 AP+P +T E R +GD AVRAA+A+GY AGTVEF+ L YFMEMNTR+QV Sbjct: 240 IAPSPQLTPEQRAYIGDLAVRAAKAVGYENAGTVEFL------LADGEVYFMEMNTRVQV 293 Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 EH +TE ITGID+V Q+R+ASG+PL KQ DI G++ + R+ AEDP FLP G++ Sbjct: 294 EHTITEEITGIDIVREQIRIASGQPLSVKQEDIQHRGFSLQFRINAEDPRNNFLPCFGKI 353 Query: 361 TELSFPEGTS-RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGT 419 T P G R D+ + G TI PYYD + KL+V AL R AL + R+ G Sbjct: 354 TRYYAPGGPGVRTDTAIYTGYTIPPYYDSMCLKLVVWALTWEEALARGSRALDDMRVQGV 413 Query: 420 VTNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPV--APGDEALALAAIFSTGA 473 T + ++ DFRSG +T +D E L + PG+ ALA+AA + A Sbjct: 414 KTTATYYQQILANPDFRSGQFNTSFVDNHPELLNYSIKRKPGELALAIAAAIAAHA 469 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: 776 Number of extensions: 45 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: 471 Length adjustment: 36 Effective length of query: 626 Effective length of database: 435 Effective search space: 272310 Effective search space used: 272310 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