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 5210426 Shew_2867 pyruvate carboxylase, propionyl-CoA carboxylase (RefSeq)
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__PV4:5210426 Length = 1094 Score = 321 bits (823), Expect = 9e-92 Identities = 203/611 (33%), Positives = 324/611 (53%), Gaps = 67/611 (10%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 +F+++L+ANRGEIA+R+ + C ++G+ ++A+Y+E D H + AD+A + R +Y Sbjct: 4 VFNRILIANRGEIAIRIAQTCADMGIDSLAIYAEDDSQSLHTKKADQAVAL-KGRGVKAY 62 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 LD E +I A+ DA+HPGYGFL+EN+ F+++ + ++G SA+ ++ LG K AR Sbjct: 63 LDIEQLIAVAKAHGCDAVHPGYGFLSENSSFSKRCHEEGICFIGSSAELLDLLGNKATAR 122 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYG--YPVAIKAEGGGGGRGLKVVHSEDEVD 178 +D P+ G +P S E+V+A G V IKA GGGGRG++ V +++ Sbjct: 123 ETALRSDTPLTGGINKPC-SLEEVQAFFTSLGDGAAVMIKALAGGGGRGMRPVSRYEDLA 181 Query: 179 GQFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKV 238 + + E F + +YVE+ ++ RHIEVQIL D G H ER+C+LQRR+QK+ Sbjct: 182 EAYRQCREEAIIAFGSGELYVEQLVQHARHIEVQILGDGTGAAVHAWERECTLQRRNQKL 241 Query: 239 IEEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV---EDGEFYFMEVNTRIQVE 295 +E APSP+L + R I E+A + +Y GT EFL+ + +FYFME+N RIQVE Sbjct: 242 LEIAPSPSLDDATRMPIIESALQLASDVKYQGLGTFEFLLDADDHSKFYFMEINPRIQVE 301 Query: 296 HTVTEEVTGLDVVKWQLRVAAGEEL-DFSQDDVEIE-GHSMEFRINAE--APEKEFAPAT 351 HT+TEE+TGL++VK Q+ + AG+ L + S + I+ G +++ RIN E P+ PA+ Sbjct: 302 HTITEEITGLNLVKLQILLGAGKTLAELSLTEAPIKRGCAIQARINLEQMLPDGSTKPAS 361 Query: 352 GTLSTYDPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDI 411 G + Y P G +R+DD + G ++ YDS+ AK+I G D L + +L +I Sbjct: 362 GVIKAYQVPNGHNVRVDDYLYAGYKVSPSYDSLGAKIIAKGEDFSAALNKVYLSLKALNI 421 Query: 412 EGLRTVIPFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEVT 471 +G+++ +L E + +T++ VE E +A D+ Sbjct: 422 DGVQSNKALLMNLLQREEVQHNRLSTRF-------------VEAHMAELLADDDHH---- 464 Query: 472 ERTFTVEVNGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREESDEGGQQVIEGD 531 E F + + + E A IP G Sbjct: 465 EHFFNIASDQQ------ETVQAVNIPAG-------------------------------- 486 Query: 532 GESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGE-GDS 590 E V + G ++ V ++ GD+V G + ++EAMKME V +E G V++VL G G+ Sbjct: 487 CEGVKSPTAGVLVQVNIESGDEVFAGQEIAVIEAMKMEIPVKSEHAGIVTEVLTGNIGEV 546 Query: 591 VDMGDVLLVLE 601 +D +L V++ Sbjct: 547 IDEHQILAVIQ 557 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: 1361 Number of extensions: 80 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: 1094 Length adjustment: 41 Effective length of query: 560 Effective length of database: 1053 Effective search space: 589680 Effective search space used: 589680 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