Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate Pf6N2E2_4278 Pyruvate carboxyl transferase subunit A (EC 6.4.1.1)
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4278 Length = 471 Score = 404 bits (1038), Expect = e-117 Identities = 213/466 (45%), Positives = 296/466 (63%), Gaps = 3/466 (0%) Query: 8 IQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYL 67 I ++L+ANRGEIA R++R+ +GI SVAV+SD DRHA HV AD A +G A P YL Sbjct: 2 ITKILIANRGEIAVRIVRACAEMGIRSVAVYSDADRHALHVKRADEAHSIG-ADPLAGYL 60 Query: 68 RGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKA 127 +++ A+ +G A+HPGYGFLSENA+ A C E G+ F+GP A I MG K+ A+ Sbjct: 61 NPRKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFIGPSAEVIRRMGDKTEARR 120 Query: 128 LMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEAL 187 M +AGVP+ PG G +E E RIGYPV+LKA +GGGG+G++ EL +A Sbjct: 121 SMIKAGVPVTPGTEGNVSGIEEALTEGDRIGYPVMLKATSGGGGRGIRRCNSREELEQAF 180 Query: 188 SSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEE 247 EA AFG A + +EK ++ P+H+E Q+ D G+ ++L ERDCSIQRR+QK++E Sbjct: 181 PRVISEATKAFGSAEVFLEKCIVNPKHIEAQILGDSFGNVVHLFERDCSIQRRNQKLIEI 240 Query: 248 APAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVTE 307 AP+P L E R +G+ +VRAA+A+GY AGTVEFLL E G+ +FMEMNTR+QVEH +TE Sbjct: 241 APSPQLTPEQRAYIGDLSVRAAKAVGYENAGTVEFLLAE-GEVYFMEMNTRVQVEHTITE 299 Query: 308 AITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREA 367 ITG+D+V QIR+A G L + QE + G A++ R+ AEDP+ +FLP+ G++ Y A Sbjct: 300 EITGIDIVREQIRIASGLPLSVKQEDIVHRGFALQFRINAEDPKNNFLPSFGKITRY-YA 358 Query: 368 AAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLA 427 GPG R D+ + G + PFYD M KL+ W T EEA R L L + + G++T A Sbjct: 359 PGGPGVRTDTAIYTGYTIPPFYDSMCLKLVVWALTWEEAMDRGLRALDDMRLQGVKTTAA 418 Query: 428 FLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEA 473 + + IL +P F + + +T F+ H + + + PE A A A Sbjct: 419 YYQEILRNPEFRSGQFNTSFVESHPELTNYSIKRKPEELALAIAAA 464 Lambda K H 0.319 0.135 0.397 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: 703 Number of extensions: 36 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: 655 Length of database: 471 Length adjustment: 36 Effective length of query: 619 Effective length of database: 435 Effective search space: 269265 Effective search space used: 269265 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 (21.8 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