Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_011382686.1 AMB_RS01215 pyruvate carboxylase
Query= reanno::SB2B:6937189 (673 letters) >NCBI__GCF_000009985.1:WP_011382686.1 Length = 1154 Score = 402 bits (1032), Expect = e-116 Identities = 226/523 (43%), Positives = 326/523 (62%), Gaps = 25/523 (4%) Query: 2 FNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGES-APASSY 60 F KLL+ANRGEIA R+ R A ++G+ TVAVYS DR A H ADES+ +G+ P +Y Sbjct: 11 FAKLLVANRGEIAIRICRAATELGLATVAVYSTEDRFALHRFKADESYLIGKGKGPIEAY 70 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L + +I + K+ G +A+HPGYGFLSEN FA A A+G+AFVGP SD + +G+K AA+ Sbjct: 71 LSIDEMIRVGKEAGCDAVHPGYGFLSENPDFADAVRAAGMAFVGPSSDVMRLLGNKVAAR 130 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 + EKAGVP++P +A +GYPL++KA++GGGG+GMR++E+E+EL+ Sbjct: 131 ALAEKAGVPVMPATGPLPADLVECKRQAAAVGYPLMLKASWGGGGRGMRVIEAETELEEL 190 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 + ARREA ++FGND++ +E+ +R+ RHVEVQ+ DSQGN V+L +RDCS+QRR+QKVVE Sbjct: 191 LAVARREAKAAFGNDEVYLEKLVRRARHVEVQILGDSQGNLVHLYERDCSVQRRNQKVVE 250 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDM-SFFFMEMNTRLQVEHPV 299 APAP L R ++ E AV A+A Y AGTVEFL+D++ +F+F+E+N R+QVEH V Sbjct: 251 RAPAPYLDGRQRSELCETAVRLARAAAYENAGTVEFLMDMETGAFYFIEVNPRVQVEHTV 310 Query: 300 TEMVTGQDLVKWQLLVAAGAQLPL------EQHEIQIHGHAFEVRIYAEDPNNEFLPASG 353 TE+VTG D+VK Q+ +A GA + +Q EI ++GHA + RI EDP N F+P G Sbjct: 311 TEVVTGIDIVKAQIRIAGGAPIGAPGSDVPKQAEIPLNGHAIQCRITTEDPANNFIPDYG 370 Query: 354 KLTFLREPEPSRHVRIDSGVR-ENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYR 412 +++ R +R+D G +I+ YYD ++ K+ W + A+AR+ RAL ++R Sbjct: 371 RISAYRGAN-GFGIRLDGGTAFSGALITRYYDSLLEKVTAWAPTPEEAIARMDRALREFR 429 Query: 413 VGGLKHNIEFLSNIAEHPAFAQANFSTDFIGRYGDALIGDSRDEADTAFVLAVLTQLRLR 472 + G+ N+ FL + EHP F ++T FI + R + T VL+ + + + Sbjct: 430 IRGVATNLTFLEAVIEHPKFVGCAYTTRFIDETPELFARQDRRDRATK-VLSFVGDVMVN 488 Query: 473 EAVSQDVAG-------HDPFSPWSSLKGFRLSSPRRHSVTLLD 508 + DVAG H P L F S P + LLD Sbjct: 489 G--NPDVAGLKRPAATHRP-----DLPAFPASEPPAGTRQLLD 524 Score = 45.1 bits (105), Expect = 2e-08 Identities = 28/72 (38%), Positives = 37/72 (51%) Query: 588 ASSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPG 647 A + D + APM G VV+ V AG V G L+ +EAMKME + A G V+ PG Sbjct: 1081 AGNADHVGAPMPGLVVSVAVHAGQAVDKGDLLVSIEAMKMETAVRADRAGTVASVAVTPG 1140 Query: 648 ELVSDGTLLLAL 659 V LL+ + Sbjct: 1141 VQVEAKDLLVIM 1152 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: 1631 Number of extensions: 73 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 673 Length of database: 1154 Length adjustment: 43 Effective length of query: 630 Effective length of database: 1111 Effective search space: 699930 Effective search space used: 699930 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: 56 (26.2 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