Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Echvi_0191 Echvi_0191 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__Cola:Echvi_0191 Length = 449 Score = 431 bits (1108), Expect = e-125 Identities = 226/450 (50%), Positives = 300/450 (66%), Gaps = 3/450 (0%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MFNK+LIANRGEIA R+IRT ++MGIKTVAVYS AD+D+ HV ADE+ +G + SY Sbjct: 1 MFNKILIANRGEIALRIIRTCKEMGIKTVAVYSTADKDSLHVRFADEAVCIGAAPSRESY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L +I A+ A+AIHPGYGFLSENA F++ CE I F+G S+ ID MG K+ AK Sbjct: 61 LNIPRVIAAAEITNADAIHPGYGFLSENAEFSKICEEYNIKFIGASSEMIDKMGDKATAK 120 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 M+ AGVP +PG G S + A ++GYP+++KA GGGG+GMRIV E E K A Sbjct: 121 ATMKAAGVPTIPGSEGLLDSIEQGIKIANEMGYPVILKATAGGGGRGMRIVREEKEFKKA 180 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 D AR+E+ ++FGND L +E+++ +PRH+E+QV D+ G +LS+RDCSIQRRHQK+VE Sbjct: 181 WDDARQESGAAFGNDGLYLEKFVEEPRHIEIQVVGDNTGKACHLSERDCSIQRRHQKLVE 240 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300 E P+P + D LR MG+AA+ A+AI Y GAGT+EFL+D +F+FMEMNTR+QVEHP+T Sbjct: 241 ETPSPFITDELRDAMGKAAIKGAEAIGYEGAGTIEFLVDKHRNFYFMEMNTRIQVEHPIT 300 Query: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360 E VT DL+K Q+ VAAG +P+ +A E RI AEDP N F P+ GK+ L Sbjct: 301 EEVTDYDLIKEQIKVAAG--IPISGQNYYPKLYAMECRINAEDPANGFRPSPGKINNLHL 358 Query: 361 PEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNI 420 P R VR+DS V +I YD MIAKLIV +SR + R+ RAL ++ + G+K I Sbjct: 359 P-GGRGVRVDSHVYAGYIIPPNYDSMIAKLIVSGQSREEVIVRMKRALEEFVIDGIKTTI 417 Query: 421 EFLSNIAEHPAFAQANFSTDFIGRYGDALI 450 F + E F NF+T F+ + ++I Sbjct: 418 PFHIALLEDEQFKAGNFTTKFLETFDFSVI 447 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: 784 Number of extensions: 39 Number of successful extensions: 3 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