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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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