Align propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized)
to candidate 207710 DVU2226 acetyl-CoA carboxylase, biotin carboxylase, putative
Query= BRENDA::P05165 (728 letters) >MicrobesOnline__882:207710 Length = 471 Score = 226 bits (575), Expect = 3e-63 Identities = 151/448 (33%), Positives = 235/448 (52%), Gaps = 43/448 (9%) Query: 65 KILVANRGEIACRVIRTCKKMGIKTVAIHSDVDASSVHVKMADEAVCVGPAPTSKSYLNM 124 K+LVANRGEIA R++R C ++G++ +++ DA+S HV++A E SY + Sbjct: 7 KVLVANRGEIATRIVRACHRLGLEFTCVYTAEDAASGHVRLARELGGANSLYRVSSYHDA 66 Query: 125 DAIMEAIKKTRAQAVHPGYGFLSENKEFARCLAAED--VVFIGPDTHAIQAMGDKIESKL 182 + ++ AVHPGYGF +E+ FAR +A + ++FIGP I+ +GDKI +K Sbjct: 67 NELLAVADDAGCTAVHPGYGFFAEDYRFARRVAQRERKLIFIGPSWRVIRELGDKINTKR 126 Query: 183 LAKKAEVNTIPGFDGVVKDAEEAVRIARE---------IGYP-VMIKASAGGGGKGMRIA 232 LA+ V T+PG D + D EA ++A+ I P V++KASAGGGG G+ Sbjct: 127 LARSLGVPTVPGSDKPIYDELEAEKVAQSLYEFQEQQGIRRPLVLVKASAGGGGMGIEEV 186 Query: 233 WDDEETRDGFRLSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHG-NALWLNERECS 291 +D + + +R A F D+ +LIE+ I + H+E+Q++ D+ G N + R CS Sbjct: 187 YDLDLFKSVYRRIRNYALRQFKDEGVLIEQRIRDFNHLEVQIVSDRTGRNPVHFGTRNCS 246 Query: 292 IQRRN-QKVVEEAPSI--------FLDAETRRAMGEQAVALARAVKYSSAGTVEFLVDSK 342 IQ QK +E AP F A+ R + ++A+AR V Y + GT E++V Sbjct: 247 IQSIGLQKRIEVAPGFDPTSIEYGFDAAQVLRDITYHSLAMARKVGYDNVGTWEWIVTRD 306 Query: 343 KNFYFLEMNTRLQVEHPVTECIT-----GLDLVQEMIRVAKGYPLRHKQADIRINGWAVE 397 + + +E+NTR+QVE+ V+ I +DL+ E IR+ G PL + Q DI G +E Sbjct: 307 GHPFLMEVNTRIQVENGVSARIARVNGQEVDLIAEQIRIGLGQPLGYGQEDITFEGVGIE 366 Query: 398 CRVYAEDPYKSFGLPSIGRLSQYQEP--------LHLPGVRVDSGIQPGSDISIYYDPMI 449 R+ AEDP F P +GR+ + P H+P + DI +DP + Sbjct: 367 YRLIAEDPDNRF-TPWVGRIDAFGWPEEDWARMYTHVP-------TEEPYDIPTEFDPNL 418 Query: 450 SKLITYGSDRTEALKRMADALDNYVIRG 477 + I +G D E +R L+ ++G Sbjct: 419 ALAIIWGKDLEEVKRRGVSFLEGLTLQG 446 Lambda K H 0.318 0.134 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: 736 Number of extensions: 36 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: 728 Length of database: 471 Length adjustment: 37 Effective length of query: 691 Effective length of database: 434 Effective search space: 299894 Effective search space used: 299894 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 (21.7 bits) S2: 53 (25.0 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