Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_011382686.1 AMB_RS01215 pyruvate carboxylase
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000009985.1:WP_011382686.1 Length = 1154 Score = 374 bits (961), Expect = e-108 Identities = 208/452 (46%), Positives = 280/452 (61%), Gaps = 12/452 (2%) Query: 2 FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAA-DSY 60 F+K+LVANRGEIA+R+ RA ELG+ TVAVYS D+ H ADE+Y IG + ++Y Sbjct: 11 FAKLLVANRGEIAIRICRAATELGLATVAVYSTEDRFALHRFKADESYLIGKGKGPIEAY 70 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L + +I ++A DA+HPGYGFL+EN +FA V + +VGPS+D M LG K AR Sbjct: 71 LSIDEMIRVGKEAGCDAVHPGYGFLSENPDFADAVRAAGMAFVGPSSDVMRLLGNKVAAR 130 Query: 121 SLMQDADVPVVPGTTE-PADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179 +L + A VPV+P T PAD E K A GYP+ +KA GGGGRG++V+ +E E++ Sbjct: 131 ALAEKAGVPVMPATGPLPADLVE-CKRQAAAVGYPLMLKASWGGGGRGMRVIEAETELEE 189 Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239 A+RE +A F N VY+EK + RH+EVQIL D GN+ HL ERDCS+QRR+QKV+ Sbjct: 190 LLAVARREAKAAFGNDEVYLEKLVRRARHVEVQILGDSQGNLVHLYERDCSVQRRNQKVV 249 Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFL--VEDGEFYFMEVNTRIQVEHT 297 E AP+P L R + E A R RAA Y NAGTVEFL +E G FYF+EVN R+QVEHT Sbjct: 250 ERAPAPYLDGRQRSELCETAVRLARAAAYENAGTVEFLMDMETGAFYFIEVNPRVQVEHT 309 Query: 298 VTEEVTGLDVVKWQLRVAAGEELDF------SQDDVEIEGHSMEFRINAEAPEKEFAPAT 351 VTE VTG+D+VK Q+R+A G + Q ++ + GH+++ RI E P F P Sbjct: 310 VTEVVTGIDIVKAQIRIAGGAPIGAPGSDVPKQAEIPLNGHAIQCRITTEDPANNFIPDY 369 Query: 352 GTLSTYDPPGGIGIRMDDAVR-QGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFD 410 G +S Y G GIR+D G I YDS++ K+ EE + R +RAL EF Sbjct: 370 GRISAYRGANGFGIRLDGGTAFSGALITRYYDSLLEKVTAWAPTPEEAIARMDRALREFR 429 Query: 411 IEGLRTVIPFHRLMLTDEAFREGSHTTKYLDE 442 I G+ T + F ++ F ++TT+++DE Sbjct: 430 IRGVATNLTFLEAVIEHPKFVGCAYTTRFIDE 461 Score = 57.4 bits (137), Expect = 3e-12 Identities = 47/157 (29%), Positives = 75/157 (47%), Gaps = 29/157 (18%) Query: 444 LDPERIEAAVERWSPEAVAGDEEEGEVTERTFTVEVNGKRFEVSLEERGAPAIPLGGASA 503 +D E+ ++ + R+ A A EE+G R E+NG+ V + +R A Sbjct: 1025 IDLEKGKSLIVRYLATAEA--EEDGS---RKVFFELNGQPRTVRVFDRKV---------A 1070 Query: 504 AASASKPSGPRKRREESDEGGQQVIEGDGESVAAEMQGTILAVEVDEGDDVEPGDTVCIL 563 A A++P G+ + V A M G +++V V G V+ GD + + Sbjct: 1071 PARAARPKAEA---------------GNADHVGAPMPGLVVSVAVHAGQAVDKGDLLVSI 1115 Query: 564 EAMKMENDVVAERGGTVSQVLVGEGDSVDMGDVLLVL 600 EAMKME V A+R GTV+ V V G V+ D+L+++ Sbjct: 1116 EAMKMETAVRADRAGTVASVAVTPGVQVEAKDLLVIM 1152 Lambda K H 0.312 0.132 0.371 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: 1362 Number of extensions: 62 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 601 Length of database: 1154 Length adjustment: 42 Effective length of query: 559 Effective length of database: 1112 Effective search space: 621608 Effective search space used: 621608 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 56 (26.2 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