Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate RR42_RS17700 RR42_RS17700 acetyl-CoA carboxylase
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__Cup4G11:RR42_RS17700 Length = 455 Score = 398 bits (1022), Expect = e-115 Identities = 210/445 (47%), Positives = 294/445 (66%), Gaps = 8/445 (1%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MF K+LIANRGEIA R+ R R++GIKTV VYS+AD++A++V LADE+ +G + SY Sbjct: 1 MFEKILIANRGEIALRIQRACRELGIKTVVVYSEADKEAKYVKLADEAVCIGPAPSPLSY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L II A+ A+AIHPGYGFLSENA FA E SG F+GP S++I MG K +AK Sbjct: 61 LNMPAIISAAEVTDAQAIHPGYGFLSENADFAERVEKSGFVFIGPTSESIRLMGDKVSAK 120 Query: 121 LIMEKAGVPLVPGYHG---DDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESEL 177 M K+GVP VPG G DD + +LA A+ +GYP++IKAA GGGG+GMR+V +E+ L Sbjct: 121 QAMIKSGVPCVPGSEGALPDDPKE--ILATARAVGYPVIIKAAGGGGGRGMRVVHTEAAL 178 Query: 178 KAAIDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQK 237 A++ R EA +FGN ++ ME++L PRHVE+Q+ AD ++L +RDCS+QRRHQK Sbjct: 179 VNAVNMTREEAGRAFGNPEVYMEKFLENPRHVEIQILADQHRQAIWLGERDCSMQRRHQK 238 Query: 238 VVEEAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEH 297 V+EEAPAP +P L +++G+ A K I YRGAGT EFL + + F+F+EMNTR+QVEH Sbjct: 239 VIEEAPAPHIPRRLIERIGDRCAEACKKIGYRGAGTFEFLYE-NNEFYFIEMNTRVQVEH 297 Query: 298 PVTEMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTF 357 PVTEM+TG D+V+ Q+ +A G +L Q ++Q+ GH+ E RI AEDP +F P+ G++T Sbjct: 298 PVTEMITGIDIVQEQIRIAFGEKLRWRQKDVQLRGHSIECRINAEDP-FKFTPSPGRITA 356 Query: 358 LREPEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLK 417 P VR+DS + + YD MI K+I + +R +A+AR+ AL + V G++ Sbjct: 357 WHMP-GGPGVRVDSHAYDGYFVPPNYDSMIGKIITYGATREQAIARMRIALSEMVVDGIQ 415 Query: 418 HNIEFLSNIAEHPAFAQANFSTDFI 442 N+ + F + S ++ Sbjct: 416 TNVPLHRELMLDANFVEGGTSIHYL 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: 699 Number of extensions: 30 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: 455 Length adjustment: 36 Effective length of query: 637 Effective length of database: 419 Effective search space: 266903 Effective search space used: 266903 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