Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_007474594.1 CMTB2_RS05295 acetyl-CoA carboxylase biotin carboxylase subunit
Query= BRENDA::Q42523 (734 letters) >NCBI__GCF_000170735.1:WP_007474594.1 Length = 447 Score = 426 bits (1096), Expect = e-123 Identities = 212/443 (47%), Positives = 304/443 (68%), Gaps = 4/443 (0%) Query: 38 IEKILVANRGEIACRIMRTAKRLGIQTVAVYSDADRDSLHVKSADEAVRIGPPSARLSYL 97 + +IL+ANRGEIA R +R +L + V +YS AD+D++++ AD AV +GP + SYL Sbjct: 4 LNRILIANRGEIALRAIRAIHKLDKEAVCIYSKADKDAIYLGFADGAVCVGPAKSSESYL 63 Query: 98 SGVTIMEAAARTGAQAIHPGYGFLSESSDFAQLCEDSGLTFIGPPASAIRDMGDKSASKR 157 + I+ AA T AI PGYGFLSE+ F ++C+ ++FIGP + M DKS +K Sbjct: 64 NIPAIITAAEMTECDAIFPGYGFLSENQTFVEVCKAHNISFIGPSLEVMELMADKSKAKE 123 Query: 158 IMGAAGVPLVPGYHGHEQDIDHMKSEAEKIGYPIIIKPTHGGGGKGMRIVQSGKDFADSF 217 +M +AGVP++PG G +DI+ K A +IGYP+I+K GGGG+GMR+V+ ++F Sbjct: 124 VMKSAGVPVIPGSEGAIKDIEEAKKVAREIGYPVILKAASGGGGRGMRVVEDESYLENAF 183 Query: 218 LGAQREAAASFGVNTILLEKYITRPRHIEVQIFGDKHGNVLHLYERDCSVQRRHQKIIEE 277 L A EA ++FG TI +EKYI +PRH+EVQI GDKHGNV+HL ERDCS+QRRHQK+IEE Sbjct: 184 LAASSEAESAFGDATIYMEKYIEKPRHVEVQILGDKHGNVIHLGERDCSLQRRHQKLIEE 243 Query: 278 APAPNISEKFRANLGQAAVSAARAVGYYNAGTVEFIVDTESDQFYFMEMNTRLQVEHPVT 337 +PA + E+ R L + AV AA+A+GYY+AGT+EF+VD + + FYFMEMNTRLQVEHPV+ Sbjct: 244 SPATILDEETRKKLHETAVKAAKAIGYYSAGTIEFLVDKDLN-FYFMEMNTRLQVEHPVS 302 Query: 338 EMIVGQDLVEWQIRVANGEPLPLSQSEVPMSGHAFEARIYAENVPKGFLPATGVLNHYRP 397 EM+ G DLVEW IRV GE +P SQ ++ + GHA E RI AE+ P+ F+P+ G + Sbjct: 303 EMVTGLDLVEWMIRVEEGEKIP-SQEKIEIKGHAIECRILAED-PEKFIPSPGKIQKLY- 359 Query: 398 VAVSPSVRVETGVEQGDTVSMHYDPMIAKLVVWGGNRGEALVKLKDCLSNFQVAGVPTNI 457 + VRV+T + G + +YD +IAK++ WG +R EA+ +K+ L F+++G+ T+I Sbjct: 360 IPGGKDVRVDTHIYAGYIIPPYYDSLIAKIITWGKDREEAIKVMKEALKEFKISGIKTSI 419 Query: 458 NFLQKLASHKEFAVGNVETHFIE 480 F K+ +++F N +T ++E Sbjct: 420 PFHLKMLENEDFLNNNYDTKYLE 442 Lambda K H 0.316 0.132 0.386 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: 806 Number of extensions: 31 Number of successful extensions: 5 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: 734 Length of database: 447 Length adjustment: 36 Effective length of query: 698 Effective length of database: 411 Effective search space: 286878 Effective search space used: 286878 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 (21.6 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