Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_012470595.1 GLOV_RS12625 pyruvate carboxylase
Query= reanno::pseudo6_N2E2:Pf6N2E2_2194 (649 letters) >NCBI__GCF_000020385.1:WP_012470595.1 Length = 1149 Score = 373 bits (957), Expect = e-107 Identities = 202/449 (44%), Positives = 285/449 (63%), Gaps = 9/449 (2%) Query: 9 LLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAA-DSYLQI 67 ++ ANRGEIA R+ R +G++TVA++S D+ + H +AD +G KA D+YL I Sbjct: 10 VMAANRGEIAIRIFRACTELGISTVALYSEEDKLSLHRYKADEAYLIGKGKAPIDAYLGI 69 Query: 68 DKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALM 127 D++IA A + AIHPGYGFL+ENA FA E AG+ F+GP A A+G K A + Sbjct: 70 DEIIALALKADVDAIHPGYGFLAENAEFAEKCEAAGITFIGPTAEMQRALGDKVAGRKAA 129 Query: 128 ETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187 +A VP+VPG + E A+ GYP+++KA AGGGG+GM+V + +L E L + Sbjct: 130 MSAEVPVVPGTEDPIEKEEEALKFAKDSGYPIIIKAAAGGGGRGMRVARNKKELLEGLVA 189 Query: 188 AQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247 A+ EA+++FG++ + +E+Y+ P+H+E+QV D +GN ++ ERDCSIQRRHQKVVE AP Sbjct: 190 ARSEAKAAFGNATVFLERYIENPKHIEVQVMGDNYGNLVHFFERDCSIQRRHQKVVEFAP 249 Query: 248 APGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAI 307 + LT Q R+ + AA++ A + Y AGTVEFL+D G F+F+EMN R+QVEH VTE I Sbjct: 250 SLCLTQQQREEICTAALKIAGQVKYRNAGTVEFLVDQEGSFYFIEMNPRIQVEHTVTEMI 309 Query: 308 TGLDLVAWQIRVAQGEPLPITQAQVP------LLGHAIEVRLYAEDPVNDFLPATGRLAL 361 TG +LV QI VAQG L + +P + G+AI+ R+ EDP N+F P G L Sbjct: 310 TGRNLVQNQILVAQGYKLSDPEINIPSQSAIDMRGYAIQCRITTEDPSNNFAPDFGTLTT 369 Query: 362 YRESAKGPGRRVDSG-VEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGL 420 YR SA G G R+D+G G +I+P YD +L K+ +WG N + A + L EF + G+ Sbjct: 370 YR-SAAGAGIRLDAGNAFTGAQITPHYDSLLVKVSSWGLNFKDAASIMHRALQEFRVRGV 428 Query: 421 KTNIGFLRRIVAHPAFAAAELDTGFIPRY 449 KTNIGFL ++ H F + DT FI ++ Sbjct: 429 KTNIGFLENVITHSVFLNGKCDTSFIEKH 457 Score = 49.7 bits (117), Expect = 7e-10 Identities = 26/73 (35%), Positives = 42/73 (57%) Query: 573 EASHSHQGGLAAPMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYC 632 +A + G + APM G +++V V G V AG L+V EAMKME +I+A G + + Sbjct: 1074 KADKGNAGHVGAPMPGKVLKVNVKAGDEVKAGDVLMVTEAMKMETNIKAKADGKVAEVKF 1133 Query: 633 QEGEMVSEGSALV 645 +EG+ V + ++ Sbjct: 1134 KEGDKVEKEDLVI 1146 Lambda K H 0.319 0.134 0.389 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: 1466 Number of extensions: 71 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 649 Length of database: 1149 Length adjustment: 42 Effective length of query: 607 Effective length of database: 1107 Effective search space: 671949 Effective search space used: 671949 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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