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_092057887.1 BQ4888_RS13975 pyruvate carboxylase
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_900111775.1:WP_092057887.1 Length = 1148 Score = 409 bits (1052), Expect = e-118 Identities = 217/450 (48%), Positives = 290/450 (64%), Gaps = 9/450 (2%) Query: 2 FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAA-DSY 60 F KV+ ANRGEIA+R+ RAC ELG++TVA+YSE DK H ADEAY IG + D+Y Sbjct: 6 FKKVMAANRGEIAIRIFRACTELGIKTVAIYSEEDKLTLHRYKADEAYLIGRGKGPIDAY 65 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L + +I+ ARK + DAIHPGYGFL+EN EFA E + +++GP+A+ +LG+K AR Sbjct: 66 LGIDEIIDLARKKEVDAIHPGYGFLSENPEFAEACERAGISFIGPTAEIQRQLGDKVAAR 125 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + A VPVVPGT +P S E+ A GYPV +KA GGGGRG++V +++ E+ Sbjct: 126 KVAVSAGVPVVPGTEKPVTSEEEALIFAKSCGYPVIVKAAAGGGGRGMRVAYNQKELLEG 185 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 ++A E +A F NASV++EKYLE P+HIEVQI+ D+HGN+ H ERDCS+QRRHQKVIE Sbjct: 186 LKSAASEAKAAFGNASVFLEKYLEKPKHIEVQIMGDKHGNIVHYFERDCSIQRRHQKVIE 245 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 APSP+LS + RE + A + + Y NAGTVEFL++ + FYF+E N RIQVEHTVT Sbjct: 246 LAPSPSLSPEKREEVCAMAMKIAGSVGYINAGTVEFLMDKEQNFYFIETNPRIQVEHTVT 305 Query: 300 EEVTGLDVVKWQLRVAAGEELD------FSQDDVEIEGHSMEFRINAEAPEKEFAPATGT 353 E VTG ++V+ Q+ VA G +L SQ D+E+ GH+++ R+ E P FAP GT Sbjct: 306 EAVTGRNLVQTQILVAEGHKLSDPEIGVGSQADIELRGHAIQCRVTTEDPANNFAPDFGT 365 Query: 354 LSTYDPPGGIGIRMDDA-VRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIE 412 L Y P G G+R+D G I YDS++ K+ G + RAL EF I Sbjct: 366 LKVYRSPAGFGVRLDAGNAYSGSRIAPHYDSLLVKITTWGLNFHTAARSMHRALQEFRIR 425 Query: 413 GLRTVIPFHRLMLTDEAFREGSHTTKYLDE 442 G++T I F ++T + F +G T YLDE Sbjct: 426 GVKTNIGFLENVITHKIFLDGLCDTSYLDE 455 Score = 63.9 bits (154), Expect = 4e-14 Identities = 32/70 (45%), Positives = 45/70 (64%) Query: 531 DGESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDS 590 D + V A M G I + V+ GD+V+ G+T+ EAMKME +V A+ G V +VL EGD Sbjct: 1078 DAKQVGAPMPGKIFKLLVNVGDEVKAGETLLSTEAMKMETNVKAKEDGVVKEVLFKEGDQ 1137 Query: 591 VDMGDVLLVL 600 V GD+L++L Sbjct: 1138 VQQGDLLVIL 1147 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: 1376 Number of extensions: 73 Number of successful extensions: 6 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: 601 Length of database: 1148 Length adjustment: 42 Effective length of query: 559 Effective length of database: 1106 Effective search space: 618254 Effective search space used: 618254 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 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