Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Pf1N1B4_225 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2194 (649 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_225 Length = 653 Score = 592 bits (1527), Expect = e-173 Identities = 332/665 (49%), Positives = 429/665 (64%), Gaps = 33/665 (4%) Query: 4 PALTTLLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADS 63 PA + +L+ANRGEIACR+ RTA+A+G TVAV S D DA H + AD V++G + S Sbjct: 2 PAFSKILIANRGEIACRIQRTAQALGYRTVAVFSDADADALHVQMADEAVNIGPAPVQQS 61 Query: 64 YLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAA 123 YL I +I AA+ +GA AIHPGYGFLSENA FARA + AG+IF+GP AI+ MGSK + Sbjct: 62 YLNIQAIIDAARRTGADAIHPGYGFLSENAEFARACQQAGIIFIGPSPEAIELMGSKRLS 121 Query: 124 KALMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183 K M AGVP + GY G QD T AERIGYP+++KA+AGGGG+GM++V +L E Sbjct: 122 KLAMIKAGVPCIKGYQGSEQDDATLSREAERIGYPLMIKASAGGGGRGMRLVHSAGELLE 181 Query: 184 ALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243 L +A+ EAQ FG +++E+ L+ PRHVE+QVF DQHGN +YL ERDCSIQRRHQK++ Sbjct: 182 QLRTARSEAQHGFGSDELILEQALIDPRHVEVQVFGDQHGNLIYLGERDCSIQRRHQKII 241 Query: 244 EEAPAPGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPV 303 EEAP P +TA LRQAMGEAA++A +A+ YVGAGTVEFLLDARG+F+F+EMNTRLQVEHPV Sbjct: 242 EEAPCPVMTADLRQAMGEAALKAGRAVNYVGAGTVEFLLDARGQFYFLEMNTRLQVEHPV 301 Query: 304 TEAITGLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDFLPATGRLALYR 363 TE ITGLDLVAWQ VA+G PLP+ Q QV L GHA+EVRLYAEDP FLP TGR+A + Sbjct: 302 TELITGLDLVAWQFHVAEGLPLPLQQEQVQLNGHAMEVRLYAEDPAQGFLPQTGRIAAWE 361 Query: 364 ESAKGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKTN 423 + G G R+D G+ EG +SPFYDPMLGKLIA G RE+AR +LL + + + G+++N Sbjct: 362 PALPG-GVRIDHGLIEGQSVSPFYDPMLGKLIAHGATREEARRKLLRAVQDSVLLGVQSN 420 Query: 424 IGFLRRIVAHPAFAAAELDTGFIPRYQAQ------LLPEPGELDDA---FWLAAAQGFAL 474 L ++ HP F + + TGFIP + A +P EL A F+ A+AQ Sbjct: 421 QRLLACLLEHPQFISGKFSTGFIPTHFADHPCLHPHVPSAEELAIAAALFYQASAQAHRT 480 Query: 475 SLAPHIRGDDAGSPWASTTGM----RLGL-SRETTLHLSCEGQDRALTLDVTAHCAELK- 528 LA W + + R+GL ++ + L+ E + + A ELK Sbjct: 481 PLA----------GWRNNASVPLHYRIGLEDQDWPVELNAE-PGKPYRAQIGARTLELKV 529 Query: 529 ----GERLTIEHHGVRRSHRAIRQGDSLYLHW-AGDLHRIDLYDPLAAAEASHSHQGGLA 583 G T+E G+R+ H + L+L G L +D L + +AS S G L Sbjct: 530 IQCDGRWATLEIDGIRQRHAYRLKAGQLWLFTRPGSLRLVDRTQALVSGQASVS-SGTLK 588 Query: 584 APMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSEGSA 643 APM+G+IV VLVS G PV G LVVLEAMKMEH +++ GV+K L + G+ V Sbjct: 589 APMDGAIVDVLVSEGSPVSKGQLLVVLEAMKMEHPLKSGIDGVLKRLQVRVGDQVKNRQI 648 Query: 644 LVAFE 648 L+ E Sbjct: 649 LLEVE 653 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: 1080 Number of extensions: 48 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: 649 Length of database: 653 Length adjustment: 38 Effective length of query: 611 Effective length of database: 615 Effective search space: 375765 Effective search space used: 375765 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: 54 (25.4 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