Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate 207299 DVU1834 pyruvate carboxylase, putative
Query= reanno::PS:Dsui_0516 (663 letters) >MicrobesOnline__882:207299 Length = 1234 Score = 322 bits (824), Expect = 9e-92 Identities = 181/447 (40%), Positives = 272/447 (60%), Gaps = 9/447 (2%) Query: 3 KKILIANRGEIACRVIKTAR-KMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61 K IL+ANRG A R+ ++ R + V ++ DK + A E + +G A +YL Sbjct: 16 KAILVANRGIPARRICRSIRERFDAVAVMTATDVDKTSPAASAAQELLLLG--ADPRAYL 73 Query: 62 VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121 D+II+ KQ G A+HPG+GF SE+ F + E G+ FIG ++ +G+K++ +K Sbjct: 74 DIDRIISLAKQRGVVAIHPGWGFASEDDRFPSKCHEAGLTFIGSTAEAMNLLGNKVQVRK 133 Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181 LA + V +PG A+D P A ++ +IG P+M+KA GGGG+G+ +++E + F Sbjct: 134 LARKLGVPVVPGSEGAVDIPTAR-KLIDEIGLPIMLKAEGGGGGRGIFAIRDESELDDAF 192 Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241 A+ SFG+ R+F+EKY+ RHIEIQV+ D +GN +ERDCSIQR HQK+IE Sbjct: 193 FKASTMAQASFGNPRLFVEKYLESVRHIEIQVIADMYGNAFAFDERDCSIQRNHQKLIEI 252 Query: 242 APSPF--VDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHP 299 PSP+ + PE+R+ + E + L R V Y S TVEF+V+ A+ E Y +E+NTRLQVEH Sbjct: 253 TPSPWPGITPELREKLKEYSKMLVREVGYHSLATVEFLVT-ASGEAYLIEVNTRLQVEHG 311 Query: 300 VTELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKF 359 +TE G+DLVE+ I VA+G +L LT+ + + AM+ RIN EDP GF P++G + ++ Sbjct: 312 ITECRYGIDLVEEQIAVAFGAQLRLTEENTKPVHHAMQVRINCEDPQAGFSPNSGLVSRY 371 Query: 360 QPPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGIS 419 P VR+D+ + G E YDS + LI +G ++ + M L+ ++I G+ Sbjct: 372 VSPG--GPGVRLDSNMCAGYEFPPNYDSAGSLLITYGQGWQKVLGIMERCLSEYIIGGLK 429 Query: 420 SNIPFQAALMQHARFQSGIFDTGFIAK 446 + IPF +M+H RF++G FDT FIA+ Sbjct: 430 TTIPFYKQVMKHPRFRAGDFDTNFIAE 456 Score = 32.0 bits (71), Expect = 2e-04 Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 3/65 (4%) Query: 585 MPEKAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKK 644 M ++A P + +P G L + V G VK GE+L + MK E + A D VK+ Sbjct: 1120 MADRANP---MHVAAPSNGDLWVMYVHPGDVVKKGEELFNVSIMKQEKAVLAPMDAMVKR 1176 Query: 645 ISVTA 649 + TA Sbjct: 1177 VLKTA 1181 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: 1791 Number of extensions: 93 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 663 Length of database: 1234 Length adjustment: 43 Effective length of query: 620 Effective length of database: 1191 Effective search space: 738420 Effective search space used: 738420 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: 56 (26.2 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