Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_011648943.1 RL_RS33695 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::PS:Dsui_0516 (663 letters) >NCBI__GCF_000009265.1:WP_011648943.1 Length = 461 Score = 408 bits (1049), Expect = e-118 Identities = 213/462 (46%), Positives = 303/462 (65%), Gaps = 12/462 (2%) Query: 3 KKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYLV 62 + +L+ANRGEIA RVIK A+ +GI+TV V+S AD D L V +ADEAV IGP A K+SYL Sbjct: 4 RSVLVANRGEIAVRVIKAAKALGIRTVQVHSAADADMLAVRLADEAVNIGPPAPKKSYLD 63 Query: 63 ADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKKL 122 + +IAA K G +AVHPGYGFLSEN +F+ + + G+ FIGP +I +GDK+ ++++ Sbjct: 64 IEAVIAAAKAAGVDAVHPGYGFLSENGDFADAVRDAGMIFIGPSGDAIRTLGDKVAARQV 123 Query: 123 AIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGFS 182 A A V T+PG + + G + A +A +IG+PVMIKA+AGGGG+G+R+ + AE + F Sbjct: 124 AKRAGVPTVPGSDGRVAGLEEARLLAGEIGFPVMIKAAAGGGGRGIRIVDSIAELEQQFP 183 Query: 183 SCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEEA 242 EA +FGD +++EK + RH+E+Q+ GD N+V+ ER+CS+QRR QKV EEA Sbjct: 184 LASAEALAAFGDGGLYLEKVIARARHVEVQIFGDGQ-NFVHFFERECSLQRRRQKVWEEA 242 Query: 243 PSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVTE 302 P+ + +MR+ + AVALAR V Y AGTVE++ T +FYF+E+NTR+QVEHPVTE Sbjct: 243 PAFMLPADMRERLCVSAVALAREVGYRGAGTVEYLYDDETGDFYFIEVNTRIQVEHPVTE 302 Query: 303 LITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQPP 362 +ITG DLV++M +VA G L + Q D+ +G A+ECRINAEDPF+ F PS G + P Sbjct: 303 MITGFDLVQEMFKVAGGAALSVAQRDIVASGHAIECRINAEDPFKAFQPSPGTIASLSVP 362 Query: 363 AEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSNI 422 E +G +R DT +Y+G I +YDS++ KLIVH +R+ + ++ +L I G+ + + Sbjct: 363 -EGEG-IRFDTMLYEGYTIPPFYDSLLGKLIVHAETRKACLEKLAASLTALAIEGVPTTV 420 Query: 423 PFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPAL 464 AL + A G F T F+ + + HD PAL Sbjct: 421 ALHLALARDASVAKGAFHTRFLEQ---------WLEHDFPAL 453 Lambda K H 0.319 0.135 0.391 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: 755 Number of extensions: 29 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: 663 Length of database: 461 Length adjustment: 36 Effective length of query: 627 Effective length of database: 425 Effective search space: 266475 Effective search space used: 266475 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 24 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