Align Propionyl-CoA carboxylase beta chain; EC 6.4.1.3 (characterized)
to candidate WP_028321998.1 H567_RS0114790 hypothetical protein
Query= SwissProt::Q168G2 (510 letters) >NCBI__GCF_000422285.1:WP_028321998.1 Length = 495 Score = 261 bits (666), Expect = 5e-74 Identities = 160/490 (32%), Positives = 263/490 (53%), Gaps = 19/490 (3%) Query: 7 QLEDRRAAARLGGGQKRIDAQHGRGKLTARERVDLLLDEGSFEEFDMFVTHRCTDFNMQD 66 + ED RA + G Q R++ +GKL +R+ +LLDEGS+ E+ F R + ++ Sbjct: 9 RFEDERAWVQRGN-QPRLERHLAKGKLHVSQRISMLLDEGSWLEYGEFA--RSVEPGFEE 65 Query: 67 QKPAGDGVVTGWGTINGRVVYVFSQDFTVLGGSVSETHSKKICKIMDMAMQNGAPVIGIN 126 + P DGV+TG G I+GR V V D TVLGG+ S +K+ +I+D+A +NG P++ ++ Sbjct: 66 RSPR-DGVMTGLGRIHGRTVAVLGDDVTVLGGTQSFVSVRKVDRIIDLATRNGFPILSLS 124 Query: 127 DSGGARIQEGVDS----LAGYGEVFQRNIMASGVVPQISM--IMGPCAGGAVYSPAMTDF 180 + GG RI +G+ S L+G V + +A+ + + + G G + M D Sbjct: 125 EGGGVRIPDGIGSGFTRLSGLETVKSLSWLANHDRRPLMLCGVFGYTYGDPAFRAGMADI 184 Query: 181 IFMVKDSSYMFVTGPDVVKTVTNEQVSAEELGGATTHTRKSSVADAAFENDVEALAEVRR 240 MV+DSS + V+ P +++ NE ++ +LGG H + D + + + + +R+ Sbjct: 185 TLMVEDSS-VAVSSPPLLQVAINETITDRDLGGPHMHETMTGTVDLVVKTEQDCIRTLRK 243 Query: 241 LVDFLPLNNREKPPVRPFFDDPDRIEPSLDTLVPDNPNTPYDMKELIHKLADEGDFYEIQ 300 ++ L + P P D PDR+ P L+T+VP N YDMK+++ ++ D G++ E++ Sbjct: 244 ILHLL------RSPESPS-DPPDRLIPDLETIVPHNNRQVYDMKKVVDRVCDHGEWIELK 296 Query: 301 EEFAKNIITGFIRLEGRTVGVVANQPLVLAGCLDIDSSRKAARFVRFCDAFEIPLLTLID 360 +F K +I G R+ GR VG++A+QP+ G +D S RK+A F+ F +IPLL + D Sbjct: 297 PKFGKGLIIGLGRIGGRAVGIMASQPMSGGGSVDAKSLRKSASFMEFASRRKIPLLVIQD 356 Query: 361 VPGFLPGTSQEYGGVIKHGAKLLYAYGEATVPMVTVITRKAYGGAYVVMSSKHLRADFNY 420 +PGFL G+ E G++ A VPMVT+I RK+YG AY + A F Sbjct: 357 IPGFLIGSEVEKDGMVNAIAAHSGTMDRVDVPMVTLIIRKSYGAAYYFLGMAATGAQFVA 416 Query: 421 AWPTAEVAVMGAK-GATEIIHRGDLGDPEKIAQHTADYEERFANPFVASERGFVDEVIQP 479 AWP AE++ + + GA + D + Q + A+ + ++ ++D +I P Sbjct: 417 AWPNAEISFIAPEMGAAILTKHADPAVKAQAQQQARADLTKSASVWDSAYEYWIDAIICP 476 Query: 480 RSTRKRVARA 489 TR+ V RA Sbjct: 477 EETRRVVCRA 486 Lambda K H 0.319 0.137 0.402 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: 603 Number of extensions: 27 Number of successful extensions: 6 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: 510 Length of database: 495 Length adjustment: 34 Effective length of query: 476 Effective length of database: 461 Effective search space: 219436 Effective search space used: 219436 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: 52 (24.6 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