Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate 207710 DVU2226 acetyl-CoA carboxylase, biotin carboxylase, putative
Query= metacyc::MONOMER-13597 (509 letters) >MicrobesOnline__882:207710 Length = 471 Score = 195 bits (496), Expect = 3e-54 Identities = 146/445 (32%), Positives = 228/445 (51%), Gaps = 36/445 (8%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 +VLVANRGEIATR+++A +G+ VY+ D + H + A E + SY + Sbjct: 7 KVLVANRGEIATRIVRACHRLGLEFTCVYTAEDAASGHVRLARELGGANSLYRVSSYHDA 66 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAV--EKAGITFIGPSSEVMRKIKDKLDGKR 123 ++ A+ A A+HPGYGF +E+ FA V + + FIGPS V+R++ DK++ KR Sbjct: 67 NELLAVADDAGCTAVHPGYGFFAEDYRFARRVAQRERKLIFIGPSWRVIRELGDKINTKR 126 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEK---------IGYP-IMVKAASGGGGVGITRV 173 LA GVPT PGSD P+ EA K+A+ I P ++VKA++GGGG+GI V Sbjct: 127 LARSLGVPTVPGSDKPIYDELEAEKVAQSLYEFQEQQGIRRPLVLVKASAGGGGMGIEEV 186 Query: 174 DNQDQLMDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYG-NYVVAWERECT 232 + D V+ R + A + F + IE+ + H+E Q++ D+ G N V R C+ Sbjct: 187 YDLDLFKSVYRRIRNYALRQFKDEGVLIEQRIRDFNHLEVQIVSDRTGRNPVHFGTRNCS 246 Query: 233 IQRRN-QKLIEEAPS-PALKME---ERESMFEPI----IKFGKLINYFTLGTFETAFSDV 283 IQ QK IE AP +E + + I + + + Y +GT+E V Sbjct: 247 IQSIGLQKRIEVAPGFDPTSIEYGFDAAQVLRDITYHSLAMARKVGYDNVGTWEWI---V 303 Query: 284 SRDF--YFLELNKRLQVEHPTTELIFR-----IDLVKLQIKLAAGEHLPFSQEDLNKRVR 336 +RD + +E+N R+QVE+ + I R +DL+ QI++ G+ L + QED+ Sbjct: 304 TRDGHPFLMEVNTRIQVENGVSARIARVNGQEVDLIAEQIRIGLGQPLGYGQEDIT--FE 361 Query: 337 GTAIEYRINAEDALNNFTGSSGFVTYYREPTGPGVRVDSGI--ESGSYVPPYYDSLVSKL 394 G IEYR+ AED N FT G + + P R+ + + E +P +D ++ Sbjct: 362 GVGIEYRLIAEDPDNRFTPWVGRIDAFGWPEEDWARMYTHVPTEEPYDIPTEFDPNLALA 421 Query: 395 IVYGESREYAIQAGIRALADYKIGG 419 I++G+ E + G+ L + G Sbjct: 422 IIWGKDLEEVKRRGVSFLEGLTLQG 446 Lambda K H 0.317 0.135 0.385 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: 532 Number of extensions: 26 Number of successful extensions: 6 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: 509 Length of database: 471 Length adjustment: 34 Effective length of query: 475 Effective length of database: 437 Effective search space: 207575 Effective search space used: 207575 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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