Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_101589346.1 BJEO58_RS10090 acyl-CoA carboxylase subunit beta
Query= SwissProt::P53003 (546 letters) >NCBI__GCF_900169175.1:WP_101589346.1 Length = 536 Score = 703 bits (1815), Expect = 0.0 Identities = 362/547 (66%), Positives = 422/547 (77%), Gaps = 12/547 (2%) Query: 1 MSSATEPVGVPPAEAPDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERID 60 MS TEP P ++ TTA ++A + A H GSERAVA Q KGK+TARERID Sbjct: 1 MSQTTEP---QPPDSSVPRTTADRIA-AFEERRTAAHTGSERAVANQRKKGKQTARERID 56 Query: 61 MLLDEGSFVELDEHARHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSL 120 LLD GSF E+DE RH +T+FGM +RP GDGVV G GT++GR V VF+ DFTV GGSL Sbjct: 57 QLLDTGSFQEVDEFVRHHNTHFGMMKNRPDGDGVVCGLGTIEGRTVAVFAHDFTVLGGSL 116 Query: 121 GEVFGEKIVKVMDLAMKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQI 180 E G KIVKV LA+K GCP++GINDSGGARIQEGV ++ L+AEIF+ N +SGVIPQI Sbjct: 117 AEANGRKIVKVQKLALKLGCPIIGINDSGGARIQEGVGSIALFAEIFRLNVASSGVIPQI 176 Query: 181 SLIMGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNER 240 SLIMGP AGGAVYSPA+TD T+MVD TSHM+ITGPDVIKTVTGE+V E+LGG RT+N Sbjct: 177 SLIMGPSAGGAVYSPALTDVTIMVDGTSHMYITGPDVIKTVTGENVGHEELGGGRTNNTV 236 Query: 241 SGNAHYLATDEDDAISYVKELLSFLPSNNLSSSPVFPG-AEVEEGSVADGVGDADLELDA 299 +GNAHYLA DE DAI YV++LLS+LP N+L P + A +EE + D LDA Sbjct: 237 TGNAHYLAEDEPDAIDYVRDLLSYLPQNSLDPVPRYDEPAHLEES-------EEDRALDA 289 Query: 300 LVPDSPNQPYDMREVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAG 359 LVPDSP+QPYD+ V+ ++D L+VS LFAPN++ FGR+EG SVG++ANQPMQLAG Sbjct: 290 LVPDSPSQPYDILRVVEAVLDPETLLQVSELFAPNVVTAFGRVEGRSVGIIANQPMQLAG 349 Query: 360 TLDIDASEKAARFVRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATV 419 TLDIDASEKAARFVR CDAFNIP+LT VDVPGFLPGT QE+ GIIRRGAKL+YAY EATV Sbjct: 350 TLDIDASEKAARFVRLCDAFNIPILTFVDVPGFLPGTDQEYGGIIRRGAKLIYAYGEATV 409 Query: 420 PLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERG 479 PLVT+ITRKAYGGAY VMGSK LGADINLAWP+AQIAVMGAQGAANI+YRR LA E G Sbjct: 410 PLVTLITRKAYGGAYCVMGSKQLGADINLAWPSAQIAVMGAQGAANIVYRRDLAAVDEAG 469 Query: 480 EDVEALRARLQQEYEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAK 539 DV+A R L QEYED L NPY+AAE GY+D+VI PS TR + R+LR L +K PA+ Sbjct: 470 GDVDARREELIQEYEDALLNPYLAAEEGYIDAVIRPSETRERIVRSLRALENKHVEQPAR 529 Query: 540 KHGNIPL 546 KHGNIPL Sbjct: 530 KHGNIPL 536 Lambda K H 0.318 0.136 0.398 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: 862 Number of extensions: 31 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: 546 Length of database: 536 Length adjustment: 35 Effective length of query: 511 Effective length of database: 501 Effective search space: 256011 Effective search space used: 256011 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: 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