Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 109 bits (273), Expect = 1e-28 Identities = 74/246 (30%), Positives = 131/246 (53%), Gaps = 17/246 (6%) Query: 65 AVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMTID 124 A++D S + +GE + ++G SGSGK++L+ IL + P + G V+ +G D+ ++ Sbjct: 17 ALDDFSLDIAEGEFVALLGPSGSGKSSLLR-ILAGLDDPDR---GDVLRDGTDLLALPAQ 72 Query: 125 EFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEA---DKKRVIERASELLKLV 181 +DI V Q AL P + +++ A ++ + R +LL+ V Sbjct: 73 R------RDIGLVFQ--HYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRV 124 Query: 182 GLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNI 241 L+ + + YP QLSGG +QRV +A +L + P L+L+DEP ALD + L ++++ Sbjct: 125 QLE--ELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDL 182 Query: 242 NQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSSIPS 301 + +G+T V VTHD ++A+R++VM +G + + G EI + P P+ V Sbjct: 183 QRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGRANR 242 Query: 302 LKGEVK 307 ++G V+ Sbjct: 243 IRGHVE 248 Lambda K H 0.319 0.138 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: 220 Number of extensions: 5 Number of successful extensions: 1 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: 362 Length of database: 384 Length adjustment: 30 Effective length of query: 332 Effective length of database: 354 Effective search space: 117528 Effective search space used: 117528 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 (21.8 bits) S2: 50 (23.9 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