Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_007474327.1 CMTB2_RS04330 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::pseudo1_N1B4:Pf1N1B4_3984 (651 letters) >NCBI__GCF_000170735.1:WP_007474327.1 Length = 476 Score = 373 bits (957), Expect = e-107 Identities = 195/445 (43%), Positives = 277/445 (62%), Gaps = 2/445 (0%) Query: 9 LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68 +L+ANRGEIA R++R K +G+T+VA+ S D + R AD + G +YL + Sbjct: 6 ILIANRGEIALRIIRACKEMGITSVAIFSEPDLNGLWVRRADEAYPILGDPIK-AYLDYE 64 Query: 69 KLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 128 ++I AK +G AIHPGYGFLSEN FARA E AG+ F+GP A ID G K A+K M+ Sbjct: 65 RIIDIAKKAGVDAIHPGYGFLSENGDFARACERAGIKFIGPRADDIDLYGDKMASKTAMK 124 Query: 129 TAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188 G+P++ G D++ ++IG+PV++KA GGGG+GM++V + E +A Sbjct: 125 KVGMPVLEGTEEPIIDIKEAEKIAKQIGFPVIIKAAFGGGGRGMRIVRSEEEFKELFEAA 184 Query: 189 QREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248 E++ FG + +EKY+ PRH+E+Q+ AD HGN ++L RDCSIQRRHQKV+E A + Sbjct: 185 TSESMKFFGRGEVFIEKYVENPRHIEVQILADTHGNVIHLGIRDCSIQRRHQKVIEIAES 244 Query: 249 PGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308 P LS + R + E +V + + +GYV AGTVEFL+D F+F+EMNTR+QVEHPV+E ++ Sbjct: 245 PSLSKDTRDKICEVSVNALKKLGYVSAGTVEFLVDENENFYFIEMNTRVQVEHPVSEVVS 304 Query: 309 GLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRESAAG 368 G+D++ IRVA GE L +TQD V + G AIE RL +EDP +F+P TG + G Sbjct: 305 GVDIIQEMIRVAEGEKLSITQDDVNIRGFAIEFRLNSEDPTKNFMPTTGTIKNLM-LPGG 363 Query: 369 PGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNINFLR 428 G R D+ + EG ++ YD M+GKLI +G+D E + LDE IGG+ TNI R Sbjct: 364 IGIRNDNALYEGYKLPTNYDSMIGKLIVYGKDWEDTVNKARRALDELNIGGVVTNIPLHR 423 Query: 429 RIIGHPAFAAAELDTGFIPRYQEQL 453 +I F + T ++ E+L Sbjct: 424 AVIRDEDFIKGKFTTKYLDEKLEKL 448 Lambda K H 0.318 0.134 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: 668 Number of extensions: 18 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: 651 Length of database: 476 Length adjustment: 36 Effective length of query: 615 Effective length of database: 440 Effective search space: 270600 Effective search space used: 270600 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 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