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 Ac3H11_4028 Biotin carboxylase of acetyl-CoA carboxylase (EC 6.3.4.14)
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4028 Length = 449 Score = 455 bits (1171), Expect = e-132 Identities = 230/449 (51%), Positives = 308/449 (68%), Gaps = 2/449 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF K+LVANRGEIA+R+ RAC ELG++ V VYSEAD+ +V+ A+EA IGPA + SY Sbjct: 1 MFKKILVANRGEIALRIQRACSELGIKAVMVYSEADRDAKYVKLAEEAVCIGPAPSPLSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I AA DA+AIHPGYGFL+ENA+FA +VE S F ++GP+ +++ +G+K A+ Sbjct: 61 LNMPAIISAAEVTDAEAIHPGYGFLSENADFAERVEKSGFQFIGPTPESIRIMGDKVSAK 120 Query: 121 SLMQDADVPVVPGTT-EPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179 M A VP VPG+ E D ++ +A GYPV IKA GGGGGRG++VVH+E + Sbjct: 121 QAMIRAGVPCVPGSEGELPDDPVQIRRIAKAVGYPVIIKAAGGGGGRGMRVVHTEAALVN 180 Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239 + K E A F N +VY+EK+L+ PRHIE+QILAD+H N +LGERDCS+QRRHQKVI Sbjct: 181 AVQMTKAEAGAAFGNPAVYMEKFLQNPRHIEIQILADKHRNAVYLGERDCSMQRRHQKVI 240 Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299 EEAP+P + L E+IGE + Y AGT EFL E+GEFYF+E+NTR+QVEH VT Sbjct: 241 EEAPAPGIPRKLIEKIGERCVAACKKIGYRGAGTFEFLYENGEFYFIEMNTRVQVEHPVT 300 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E +TG+D+VK Q+ VAAGE+L F+Q +EI GH++E R+NAE P K F P+ G ++T+ P Sbjct: 301 EWITGVDIVKTQIMVAAGEKLPFTQRQIEIRGHAIECRVNAEDPYK-FVPSPGRITTWHP 359 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG G+R+D + +YDSMI K+IV G RE+ L R AL+E IEG+ T +P Sbjct: 360 PGGPGVRVDSHAYTNYFVPPNYDSMIGKIIVHGDTREQALARMRTALSETVIEGINTNVP 419 Query: 420 FHRLMLTDEAFREGSHTTKYLDEVLDPER 448 HR ++ D F G YL+E L + Sbjct: 420 LHRELMVDAKFMAGGTNIHYLEEWLSQHK 448 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: 654 Number of extensions: 25 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: 449 Length adjustment: 35 Effective length of query: 566 Effective length of database: 414 Effective search space: 234324 Effective search space used: 234324 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