Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 350977 BT1449 biotin carboxylase (NCBI ptt file)
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__Btheta:350977 Length = 503 Score = 446 bits (1148), Expect = e-130 Identities = 224/442 (50%), Positives = 304/442 (68%), Gaps = 2/442 (0%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 M K+L+ANRGEIA R+ RT R M I TVAVY+ DR A HV A+E++ + S +SY Sbjct: 1 MIKKILVANRGEIAMRIFRTCRVMDISTVAVYTHVDRGALHVRYAEEAYCISNSPEDTSY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L+ ELI+ IAKK GA AIHPGYGFLSENA FAR CE G+ F+GPG+D I MG K+ A+ Sbjct: 61 LKPELILAIAKKTGA-AIHPGYGFLSENADFARRCEEEGVIFIGPGADIIAKMGIKTEAR 119 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 IM +AG+P+VPG Q + AK++GYP+++KA GGGGKGMR+V SE E + A Sbjct: 120 KIMREAGLPIVPGTETPVQGIEEVKKVAKEVGYPIMLKALAGGGGKGMRLVRSEEEAETA 179 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 + ++ EA +SFGND + +E+Y+ P H+EVQ+ D GN V+L +R+CSIQRR+QKV+E Sbjct: 180 LRLSQSEAGTSFGNDAVYIEKYIENPHHIEVQIMGDKYGNVVHLGERECSIQRRNQKVIE 239 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300 E+P+P + D RK+M + AV A K I Y AGT+EF++D D +F+F+EMNTRLQVEHPVT Sbjct: 240 ESPSPFVKDETRKKMLKVAVEACKRIGYYSAGTLEFMMDKDQNFYFLEMNTRLQVEHPVT 299 Query: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360 E TG DLV+ + VAAG LP +Q +I+ G A E RIYAEDP N F+P+ G +T +RE Sbjct: 300 EECTGVDLVRDMITVAAGNPLPYKQEDIKFSGAAIECRIYAEDPENNFMPSPGVIT-VRE 358 Query: 361 PEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNI 420 R++R+DS +S +YDPMIAKL W +R A++ + RAL +Y++ G+K I Sbjct: 359 APEGRNLRLDSAAYAGFEVSLHYDPMIAKLCCWGRTRESAISNMARALREYKILGIKTTI 418 Query: 421 EFLSNIAEHPAFAQANFSTDFI 442 F + ++ AF + + T FI Sbjct: 419 PFHQRVLKNAAFLEGKYDTTFI 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: 774 Number of extensions: 27 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: 503 Length adjustment: 36 Effective length of query: 637 Effective length of database: 467 Effective search space: 297479 Effective search space used: 297479 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