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 Dsui_0389 Dsui_0389 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__PS:Dsui_0389 Length = 455 Score = 449 bits (1155), Expect = e-130 Identities = 227/456 (49%), Positives = 310/456 (67%), Gaps = 4/456 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+L+ANRGEIA+RV RAC ELG++TV V+SEAD+ +V+ ADE+ IGPA +A SY Sbjct: 1 MFEKILIANRGEIALRVQRACRELGIKTVVVHSEADREAKYVKLADESVCIGPASSALSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I AA DA AIHPGYGFL+ENA+FA +VE S F ++GP A+ + +G+K A+ Sbjct: 61 LNIPAIISAAEVTDAQAIHPGYGFLSENADFAERVESSGFVFIGPRAETIRLMGDKVSAK 120 Query: 121 SLMQDADVPVVPGTTE--PADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVD 178 M+ A VP VPG+ P D E +K + GYPV IKA GGGGGRG++VVH+E + Sbjct: 121 DAMKAAGVPCVPGSDGALPEDPKEIIK-IGRAVGYPVIIKAAGGGGGRGMRVVHTEAALI 179 Query: 179 GQFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKV 238 ++E + F N VY+EK+LE PRH+E+Q+LADE N +LGERDCS+QRRHQKV Sbjct: 180 NAVAMTRQEAQTAFGNPMVYMEKFLENPRHVEIQVLADEFKNAVYLGERDCSMQRRHQKV 239 Query: 239 IEEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTV 298 IEEAP+P + L R+GE R Y AGT EFL E+GEFYF+E+NTR+QVEH V Sbjct: 240 IEEAPAPGIPARLIARVGERCAEACRRIGYRGAGTFEFLYENGEFYFIEMNTRVQVEHPV 299 Query: 299 TEEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYD 358 TE +TG+D+V+ Q+R+AAGE+L F Q D++ GH++E R+NAE P F P+ GT+S + Sbjct: 300 TELITGIDIVQEQIRIAAGEKLRFKQRDIQFRGHAIECRVNAEDP-FTFVPSPGTISWWH 358 Query: 359 PPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVI 418 PPGG G+R+D G ++ YDSMI K+I G RE+ + R AL+E ++G++T I Sbjct: 359 PPGGPGVRVDSHAYSGYKVPPHYDSMIGKIITFGDTREQAIRRMRIALSETVVQGIKTNI 418 Query: 419 PFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVE 454 P H+ ++ D F EG + YL+ L + +VE Sbjct: 419 PLHQELMQDARFVEGGTSIHYLEHKLAAKNEVKSVE 454 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: 643 Number of extensions: 19 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: 601 Length of database: 455 Length adjustment: 35 Effective length of query: 566 Effective length of database: 420 Effective search space: 237720 Effective search space used: 237720 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: 52 (24.6 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