Align propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized)
to candidate 8500054 DvMF_0817 Biotin carboxylase (RefSeq)
Query= BRENDA::P05165 (728 letters) >FitnessBrowser__Miya:8500054 Length = 472 Score = 240 bits (613), Expect = 1e-67 Identities = 162/462 (35%), Positives = 248/462 (53%), Gaps = 35/462 (7%) Query: 65 KILVANRGEIACRVIRTCKKMGIKTVAIHSDVDASSVHVKMADEAVCVGPAPTSKSYLNM 124 K+LVANRGEIA R+++ C+K+G+ +++ DA+S HV++A E SY + Sbjct: 7 KVLVANRGEIAIRIVQACRKLGLAFTCVYTAEDAASGHVRIARELGGDKSLCRVSSYHDA 66 Query: 125 DAIMEAIKKTRAQAVHPGYGFLSENKEFARCLAAED--VVFIGPDTHAIQAMGDKIESKL 182 + +M A AVHPGYGF +E+ FAR ++ D ++FIGP I+ +GDKI +K Sbjct: 67 NELMAVADDAGATAVHPGYGFFAEDYRFARRVSQRDRKLIFIGPSWRVIRELGDKINTKR 126 Query: 183 LAKKAEVNTIPGFDGVVKDAEEAVRIARE---------IGYP-VMIKASAGGGGKGMRIA 232 LA+ V T+PG D + D EA ++A+ I P V++KASAGGGG G+ Sbjct: 127 LARSLGVPTVPGSDRPIYDEMEAEKVAQSLFEFQEQQGIRKPLVLVKASAGGGGMGIEEV 186 Query: 233 WDDEETRDGFRLSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHG-NALWLNERECS 291 +D + R +R A F D+ +LIE+ I + H+E+QV+ D+ G N + R CS Sbjct: 187 YDIDLFRSVYRRIRNYALRQFKDEGVLIEQRIRDFNHLEVQVVSDRSGRNPVHFGTRNCS 246 Query: 292 IQRRN-QKVVEEAPSI--------FLDAETRRAMGEQAVALARAVKYSSAGTVEFLVDSK 342 IQ QK +E AP F A+ R + + ++A+AR V Y + GT E++V Sbjct: 247 IQSTGLQKRIEIAPGFDPSSIEYGFDAAQVLRDITQHSLAMARKVGYDNVGTWEWIVTRD 306 Query: 343 KNFYFLEMNTRLQVEHPVTECIT------GLDLVQEMIRVAKGYPLRHKQADIRINGWAV 396 + +E+NTR+QVE+ V+ I G+DL+ E IR+ G PL + Q D+ G + Sbjct: 307 GRPFLMEVNTRIQVENGVSATIARVRGQKGVDLIAEQIRIGLGEPLGYGQEDVTFEGVGI 366 Query: 397 ECRVYAEDPYKSFGLPSIGRLSQYQEPLHLPGVRVDSGIQPGS--DISIYYDPMISKLIT 454 E R+ AEDP F P +GR+ + P P + + + + DI +DP ++ I Sbjct: 367 EYRLIAEDPDNRF-TPWVGRVDGFGWP-ERPWLAMHTHVPSDDPYDIPTEFDPNLALAII 424 Query: 455 YGSDRTEALKRMADALDNYVIRGVTHNIALLREVIINSRFVK 496 +G D EA +R + LD V+ G + LR N RF++ Sbjct: 425 WGKDLAEARERGVEFLDTLVLEGANNAGEPLRS---NVRFLR 463 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: 748 Number of extensions: 37 Number of successful extensions: 7 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: 472 Length adjustment: 37 Effective length of query: 691 Effective length of database: 435 Effective search space: 300585 Effective search space used: 300585 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