Align Electron transfer protein (characterized, see rationale)
to candidate 350146 BT0618 Na+-transporting NADH:ubiquinone oxidoreductase, Electron transport complex protein rnfC (NCBI ptt file)
Query= uniprot:E3PU00 (428 letters) >FitnessBrowser__Btheta:350146 Length = 445 Score = 146 bits (369), Expect = 1e-39 Identities = 102/325 (31%), Positives = 162/325 (49%), Gaps = 25/325 (7%) Query: 4 VLLLKQHVGAPCQSIVEAGQKVQKGELIAKPNG-LGANLHSSVYGVVKAVN--------- 53 V+LL QH+GAP + IV G V+ G IA+P G + A +HSSV G V ++ Sbjct: 33 VILLGQHIGAPAKPIVAKGDMVKVGTKIAEPAGFVSAAIHSSVSGKVAKIDTVVDASGYA 92 Query: 54 ETAIIIEADENQPDEFVKIKDTNTH---------IEAIQEAGIVGSGGAGFPTHVKL--N 102 + AI I+ + ++ +E + T ++ I +AGIVG GGA FPT VKL Sbjct: 93 KPAIFIDVEGDEWEETIDRSKTLVKECELSSEEIVKKIADAGIVGLGGACFPTQVKLCPP 152 Query: 103 VNLEGGYVIANGAECEPVLGHNIKLMEEDPQLIIRGLKYVKEITNASKAYIAMKAKHRKA 162 + + VI N ECEP L + +LM E + ++ G+ + + +KA+I ++ A Sbjct: 153 PSFKAECVIINAVECEPYLTADHQLMLEHAEEVMVGVSILMKAVKVNKAFIGIENNKPDA 212 Query: 163 LRILKTACELEPDIEVKILPDMYPAGDERAIVRDILGVLLEPGQLPKAANAVIQNVETLK 222 + ++ IEV L YP G E+ ++ I + G LP + AV+QNV T Sbjct: 213 IELMTKVASSYAGIEVVPLKVKYPQGGEKQLIDAITKRQVASGALPISTGAVVQNVGTAF 272 Query: 223 HIVNAIELRKPYITKDITVAGRVMDATDGKVFMDVPVGESVKKYIDLCGGYMNPHGEIVM 282 + A++ KP + ITV G+ + + +G +K+ ID CGG G+++ Sbjct: 273 AVYEAVQKNKPLFERVITVTGKSVAKPSNFL---ARIGTPMKQLIDACGGLPEDTGKVIG 329 Query: 283 GGPFTGRHVEE-DAPITKTTGGILV 306 GGP G+ + + P K + GIL+ Sbjct: 330 GGPMMGKALMNIEVPTAKGSSGILI 354 Lambda K H 0.318 0.137 0.399 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: 500 Number of extensions: 28 Number of successful extensions: 4 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: 428 Length of database: 445 Length adjustment: 32 Effective length of query: 396 Effective length of database: 413 Effective search space: 163548 Effective search space used: 163548 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: 51 (24.3 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