Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_090440351.1 BLS63_RS04465 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::SB2B:6937189 (673 letters) >NCBI__GCF_900100495.1:WP_090440351.1 Length = 449 Score = 410 bits (1053), Expect = e-119 Identities = 219/443 (49%), Positives = 295/443 (66%), Gaps = 4/443 (0%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 M K+LIANRGEIA R++R +++GIKTVAV+S ADR+ H+ALADES +G ++ A SY Sbjct: 1 MLEKVLIANRGEIALRILRACKELGIKTVAVHSTADRELMHLALADESVCIGPASGALSY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L II A+ GA AIHPGYGFL+ENA FA E SG AF+GP ++ I MG K +AK Sbjct: 61 LNIPAIISAAEVTGATAIHPGYGFLAENADFAEQVENSGFAFIGPKAETIRLMGDKVSAK 120 Query: 121 LIMEKAGVPLVPGYHGD-DQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKA 179 M++AGVP+VPG G + + T LA A+++GYP++IKAA GGGG+GMR+V +E +L Sbjct: 121 DAMKRAGVPVVPGSDGPLPEDEETALAIAREVGYPVIIKAAGGGGGRGMRVVHNEEDLIK 180 Query: 180 AIDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVV 239 + R EA + FGN + +E++L PRHVEVQV +D QGN ++L DRDCS+QRRHQKV+ Sbjct: 181 SAKLTRSEAGAVFGNPMVYLEKFLGNPRHVEVQVLSDGQGNAIHLGDRDCSLQRRHQKVL 240 Query: 240 EEAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPV 299 EEAPAP + + R ++ + V A I YRGAGT EFL + D F+F+EMNTR+QVEHPV Sbjct: 241 EEAPAPLIDEQARAEVLDRCVRACIEIGYRGAGTFEFLYE-DGRFYFIEMNTRVQVEHPV 299 Query: 300 TEMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLR 359 TEMVTG D+VK L +AAG +L ++Q ++ I GHA E RI AEDP+N F+P GK+ Sbjct: 300 TEMVTGIDIVKEMLSIAAGNKLSIKQEDVVIRGHALECRINAEDPDN-FMPCPGKVKHFH 358 Query: 360 EPEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHN 419 P VR+DS + + YD +I KLI + +R ALAR+ AL + V G+K N Sbjct: 359 AP-GGNGVRVDSHLYSGYTVPPNYDSLIGKLITYGATRDEALARMRNALDEIVVDGIKTN 417 Query: 420 IEFLSNIAEHPAFAQANFSTDFI 442 I + F + + ++ Sbjct: 418 IPLHRELVIDKGFRKGGVNIHYL 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: 746 Number of extensions: 35 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 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