Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate WP_068006658.1 PsAD2_RS13240 biotin/lipoyl-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3984 (651 letters) >NCBI__GCF_001623255.1:WP_068006658.1 Length = 629 Score = 528 bits (1361), Expect = e-154 Identities = 298/646 (46%), Positives = 405/646 (62%), Gaps = 28/646 (4%) Query: 8 TLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQI 67 ++LVANRGEIA RV RTA+ G ++AV+S D A H +AD+ +GG+ A+SYL I Sbjct: 4 SVLVANRGEIARRVFRTARQKGYRSIAVYSEADATAPHVGDADVAACIGGATPAESYLNI 63 Query: 68 DKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALM 127 + ++ AA+ +GAQA+HPGYGFL+ENA FA+A +AAGL+F+GPPA AI+ MGSK +K M Sbjct: 64 EAVLEAARKTGAQAVHPGYGFLAENADFAKACDAAGLVFVGPPAQAIELMGSKRLSKLRM 123 Query: 128 ETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALAS 187 AGVP VPGY G Q E RIG P+++KA+AGGGG+G+++VE++ L + LA+ Sbjct: 124 IEAGVPCVPGYSGADQSTEVLAAEAARIGVPLMIKASAGGGGRGLRLVENLEGLEDKLAA 183 Query: 188 AQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAP 247 A EA+ +FG+ +++EK ++ PRHVEIQ+FAD HGN ++L ERDCS+QRRHQKV+EEAP Sbjct: 184 AASEAVGAFGNGELILEKAVINPRHVEIQIFADNHGNVVHLGERDCSVQRRHQKVIEEAP 243 Query: 248 APGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAI 307 P ++PE+R AMG+AAV +A+AIGY GAGTVEFLL A G F+FMEMNTRLQVEHPVTE I Sbjct: 244 GPSVTPEIRDAMGQAAVEAARAIGYRGAGTVEFLLAADGSFYFMEMNTRLQVEHPVTEEI 303 Query: 308 TGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRESAA 367 TG DLVAWQ+ VA G+ LP+ Q+ + GHA+E+RLYAED FLP TG++ + Sbjct: 304 TGQDLVAWQLDVAAGKPLPLAQEDISFSGHAMELRLYAEDADAGFLPQTGQVVAWN---- 359 Query: 368 GP--GRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNIN 425 GP RVDS +E+G IS +YDPM+ KLIA G DRE+AR +LL LD+ + GL N + Sbjct: 360 GPELALRVDSAIEQGSVISSYYDPMIAKLIAHGADREEARRKLLRGLDQLVLQGLVHNGS 419 Query: 426 FLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRADDL 485 FL+ ++ FAA E T F+ +E A + + A FA+++ T Sbjct: 420 FLKSVLLDDVFAAGEATTAFL-NDRELGSVAADSVRELMRDLAVHLFARNKGQTRWTTAT 478 Query: 486 SSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGLRRQHR 545 P I + P E L EQD LG L+ +G+RR Sbjct: 479 PLPVKIKLDGESVTPRE---DLQILEQD---DLGK------------LVFYVDGVRRS-A 519 Query: 546 AIRRGDT--LYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVE 603 + +G ++ DG+ + E + + + + APM G++V + E G V Sbjct: 520 FVSKGPEGGFWISLDGQTQFFEEQSLSTRKTDNSATSSSVIAPMPGAVVALKTEQGAQVS 579 Query: 604 AGAQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVELE 649 G L+VLEAMKM+H + AP GI+ L QEG V+ LV LE Sbjct: 580 KGDVLLVLEAMKMQHELTAPRDGIVAELGTQEGAQVNSRDVLVRLE 625 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: 930 Number of extensions: 29 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: 629 Length adjustment: 38 Effective length of query: 613 Effective length of database: 591 Effective search space: 362283 Effective search space used: 362283 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: 54 (25.4 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