Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_068006658.1 PsAD2_RS13240 biotin/lipoyl-binding protein
Query= SwissProt::Q5LUF3 (681 letters) >NCBI__GCF_001623255.1:WP_068006658.1 Length = 629 Score = 449 bits (1156), Expect = e-130 Identities = 277/684 (40%), Positives = 382/684 (55%), Gaps = 62/684 (9%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF+ +L+ANRGEIA RV +TAR+ G ++A+YS+AD A HV AD A IG +SY Sbjct: 1 MFDSVLVANRGEIARRVFRTARQKGYRSIAVYSEADATAPHVGDADVAACIGGATPAESY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 + I+ V+ A R TGAQAVHPGYGFL+EN+ FA+A +A G++FVGPP AIE MG K SK Sbjct: 61 LNIEAVLEAARKTGAQAVHPGYGFLAENADFAKACDAAGLVFVGPPAQAIELMGSKRLSK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 EA V VPGY G + + + +IG P+MIKASAGGGG+G+R+ N + + Sbjct: 121 LRMIEAGVPCVPGYSGADQSTEVLAAEAARIGVPLMIKASAGGGGRGLRLVENLEGLEDK 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 ++ +EA +FG+ + +EK V PRH+EIQ+ D+HGN ++LGER+CS+QRR+QKV+E Sbjct: 181 LAAAASEAVGAFGNGELILEKAVINPRHVEIQIFADNHGNVVHLGERDCSVQRRHQKVIE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAP P + R AMG+ AV A+A+GY AGTVEF++ +FYF+EMNTRLQVEHPVT Sbjct: 241 EAPGPSVTPEIRDAMGQAAVEAARAIGYRGAGTVEFLLAADGSFYFMEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 E ITG DLV + VAAG+PL + Q D+ +G A+E RLYAED GFLP G++ + Sbjct: 301 EEITGQDLVAWQLDVAAGKPLPLAQEDISFSGHAMELRLYAEDADAGFLPQTGQVVAWNG 360 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 P E A+R D+ + +G IS YYDPMIAKL R A Sbjct: 361 P---------------------ELALRVDSAIEQGSVISSYYDPMIAKLIAHGADREEAR 399 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 + LD ++G+ HN FL +V+ F +G+ TTAF L + +L Sbjct: 400 RKLLRGLDQLVLQGLVHNGSFLKSVLLDDVFAAGEATTAF-------------LNDRELG 446 Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGSTVSFD 540 VAA + V E+ R ++ + T W PV I D + T D Sbjct: 447 SVAADS-----VRELMRDLAVHLFARNKGQ--TRWTT---ATPLPVKIKLDGESVTPRED 496 Query: 541 DGSSMRVTSDWTPGDQLANLM--VDGAPLVLKVGK-ISGGFRIRTRGADLKVHVRTPRQA 597 +++ D L L+ VDG V K GGF I G +T Sbjct: 497 ----LQILEQ----DDLGKLVFYVDGVRRSAFVSKGPEGGFWISLDG-------QTQFFE 541 Query: 598 ELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKK 657 E + + TS ++ PMPG +V + E G +V +G L +EAMKM++ L A + Sbjct: 542 EQSLSTRKTDNSATSSSVIAPMPGAVVALKTEQGAQVSKGDVLLVLEAMKMQHELTAPRD 601 Query: 658 GVVAKINASAGNSLAVDDVIMEFE 681 G+VA++ G + DV++ E Sbjct: 602 GIVAELGTQEGAQVNSRDVLVRLE 625 Lambda K H 0.317 0.134 0.387 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: 950 Number of extensions: 37 Number of successful extensions: 3 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: 681 Length of database: 629 Length adjustment: 38 Effective length of query: 643 Effective length of database: 591 Effective search space: 380013 Effective search space used: 380013 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