Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF987 Psest_1019 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__psRCH2:GFF987 Length = 449 Score = 412 bits (1059), Expect = e-119 Identities = 217/445 (48%), Positives = 296/445 (66%), Gaps = 8/445 (1%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 M K+LIANRGEIA RV+R +++GIKTVAV+S ADRD HV+LADES +G +A A SY Sbjct: 1 MLEKVLIANRGEIALRVLRACKELGIKTVAVHSTADRDLMHVSLADESVCIGPAASAKSY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L +I A+ GA+ IHPGYGFL+ENA FA E SG F+GP +D I MG K +AK Sbjct: 61 LSIPALIAAAEVTGADGIHPGYGFLAENADFAEQVEKSGFTFIGPTADVIRLMGDKVSAK 120 Query: 121 LIMEKAGVPLVPGYHG---DDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESEL 177 M++AGVP VPG G +D+ +A L A+++GYP++IKAA GGGG+GMR+V E +L Sbjct: 121 DAMKQAGVPTVPGSDGPLPEDEKEA--LRIAREVGYPVIIKAAGGGGGRGMRVVHKEEDL 178 Query: 178 KAAIDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQK 237 A+ R EA ++FGN + +E++L PRHVE+QV AD QGN ++L DRDCS+QRRHQK Sbjct: 179 IASAKLTRNEAGAAFGNPMVYLEKFLTNPRHVEIQVLADGQGNAIHLGDRDCSLQRRHQK 238 Query: 238 VVEEAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEH 297 V+EEAPAP + + R+++ V A I YRGAGT EFL + D +F+F+EMNTR+QVEH Sbjct: 239 VIEEAPAPLIDEEARRKVQARCVKACIDIGYRGAGTFEFLYE-DGNFYFIEMNTRVQVEH 297 Query: 298 PVTEMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTF 357 PVTEMVTG D+VK LL+ G +L ++Q ++ I GHA E RI AEDP F+P+ GK+ Sbjct: 298 PVTEMVTGIDIVKEMLLIGGGQKLSIKQEDVVIRGHAVECRINAEDPRT-FMPSPGKVKH 356 Query: 358 LREPEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLK 417 P VR+DS + + + +YD +I KLI + +R A+ R+ AL + V G+K Sbjct: 357 FHAP-GGNGVRVDSHLYDGYSVPPHYDSLIGKLITFGANRDEAMGRMRNALDELIVDGIK 415 Query: 418 HNIEFLSNIAEHPAFAQANFSTDFI 442 N ++ P F + + ++ Sbjct: 416 TNAPLHRDLVRDPGFCKGGVNIHYL 440 Lambda K H 0.317 0.134 0.380 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: 777 Number of extensions: 38 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: 673 Length of database: 449 Length adjustment: 36 Effective length of query: 637 Effective length of database: 413 Effective search space: 263081 Effective search space used: 263081 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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