Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Ac3H11_4028 Biotin carboxylase of acetyl-CoA carboxylase (EC 6.3.4.14)
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4028 Length = 449 Score = 414 bits (1065), Expect = e-120 Identities = 215/421 (51%), Positives = 289/421 (68%), Gaps = 4/421 (0%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MF K+L+ANRGEIA R+ R ++GIK V VYS+ADRDA++V LA+E+ +G + SY Sbjct: 1 MFKKILVANRGEIALRIQRACSELGIKAVMVYSEADRDAKYVKLAEEAVCIGPAPSPLSY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L II A+ AEAIHPGYGFLSENA FA E SG F+GP ++I MG K +AK Sbjct: 61 LNMPAIISAAEVTDAEAIHPGYGFLSENADFAERVEKSGFQFIGPTPESIRIMGDKVSAK 120 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAE-AKKIGYPLLIKAAYGGGGKGMRIVESESELKA 179 M +AGVP VPG G+ D + AK +GYP++IKAA GGGG+GMR+V +E+ L Sbjct: 121 QAMIRAGVPCVPGSEGELPDDPVQIRRIAKAVGYPVIIKAAGGGGGRGMRVVHTEAALVN 180 Query: 180 AIDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVV 239 A+ + EA ++FGN + ME++L+ PRH+E+Q+ AD N VYL +RDCS+QRRHQKV+ Sbjct: 181 AVQMTKAEAGAAFGNPAVYMEKFLQNPRHIEIQILADKHRNAVYLGERDCSMQRRHQKVI 240 Query: 240 EEAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPV 299 EEAPAPG+P L +++GE VAA K I YRGAGT EFL + + F+F+EMNTR+QVEHPV Sbjct: 241 EEAPAPGIPRKLIEKIGERCVAACKKIGYRGAGTFEFLYE-NGEFYFIEMNTRVQVEHPV 299 Query: 300 TEMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLR 359 TE +TG D+VK Q++VAAG +LP Q +I+I GHA E R+ AEDP +F+P+ G++T Sbjct: 300 TEWITGVDIVKTQIMVAAGEKLPFTQRQIEIRGHAIECRVNAEDP-YKFVPSPGRIT-TW 357 Query: 360 EPEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHN 419 P VR+DS N + YD MI K+IV ++R +ALAR+ AL + + G+ N Sbjct: 358 HPPGGPGVRVDSHAYTNYFVPPNYDSMIGKIIVHGDTREQALARMRTALSETVIEGINTN 417 Query: 420 I 420 + Sbjct: 418 V 418 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: 37 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