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_092345839.1 BLU87_RS06260 pyruvate carboxylase
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_900107645.1:WP_092345839.1 Length = 1150 Score = 379 bits (974), Expect = e-109 Identities = 203/463 (43%), Positives = 287/463 (61%), Gaps = 11/463 (2%) Query: 2 FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAA-DSY 60 F K++ ANRGEIA+R+ RAC ELG+ TVA+YS D+ H ADEAY IG + D+Y Sbjct: 6 FKKIMAANRGEIAIRIFRACTELGISTVAIYSNEDRLSLHRYKADEAYLIGQGKGPIDAY 65 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L + +I+ ARK D DAIHPGYGFL+EN EF+ E + ++GP + +RLG K R Sbjct: 66 LGIDEIIDLARKKDVDAIHPGYGFLSENPEFSLACERAGIAFIGPPPEIQQRLGNKVSGR 125 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + +A VP+VPGT P ++ E+ A GYP+ +KA GGGGRG++V ++ E+ Sbjct: 126 QVAVEAGVPIVPGTDSPVETEEEALIFAKSCGYPIIVKASSGGGGRGMRVAQNQKELLEG 185 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 ++A E +A F +A++++EKY+E+P+HIEVQIL D+HG++ H ERDCS+QRRHQKVIE Sbjct: 186 LKSAASEAQAAFGDATIFLEKYIESPKHIEVQILGDKHGHLVHFYERDCSIQRRHQKVIE 245 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 APS L++ +R + A + + Y NAGT+EFL++ + FYF+EVN RIQVEHTVT Sbjct: 246 IAPSLDLTQKMRTEVCGYALKIAKTVGYVNAGTIEFLLDKERNFYFIEVNPRIQVEHTVT 305 Query: 300 EEVTGLDVVKWQLRVAAGEELD------FSQDDVEIEGHSMEFRINAEAPEKEFAPATGT 353 E VT ++V+ Q+RVA G L +Q D+E+ G +++ RI E P FAP GT Sbjct: 306 ELVTMRNLVQVQIRVAEGYRLADPEIGIKNQKDIELRGFAIQSRITTEDPNNNFAPDFGT 365 Query: 354 LSTYDPPGGIGIRMDDAV-RQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIE 412 + Y G G+R+D A G I YDS++ K+ G E RAL EF I Sbjct: 366 IKAYRTAAGFGVRLDAAAGYAGAHISPHYDSLLVKISTWGLTFLEAAKIMHRALQEFRIR 425 Query: 413 GLRTVIPFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVER 455 G++T I F ++T F EG+ T +LD P+ E +++ Sbjct: 426 GVKTNIGFLEKVMTYPVFLEGNCDTSFLDN--HPKLFELRIKK 466 Score = 63.9 bits (154), Expect = 4e-14 Identities = 28/71 (39%), Positives = 44/71 (61%) Query: 531 DGESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDS 590 + + + A M G I + V+ GD VE GD + + EAMKME ++ A + G + +++ EGD Sbjct: 1080 NSKEIGAPMPGKIFKLLVNVGDQVEVGDVLLVTEAMKMETNIKARKNGVIQEIIFAEGDH 1139 Query: 591 VDMGDVLLVLE 601 V GD+LL+ E Sbjct: 1140 VGQGDLLLIFE 1150 Score = 30.8 bits (68), Expect = 3e-04 Identities = 16/44 (36%), Positives = 25/44 (56%) Query: 558 DTVCILEAMKMENDVVAERGGTVSQVLVGEGDSVDMGDVLLVLE 601 +T +L ++ A G + ++LV GD V++GDVLLV E Sbjct: 1070 ETSHVLADPDNSKEIGAPMPGKIFKLLVNVGDQVEVGDVLLVTE 1113 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: 1275 Number of extensions: 55 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: 3 Length of query: 601 Length of database: 1150 Length adjustment: 42 Effective length of query: 559 Effective length of database: 1108 Effective search space: 619372 Effective search space used: 619372 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