Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate H281DRAFT_05805 H281DRAFT_05805 dipeptide transport system ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Burk376:H281DRAFT_05805 Length = 334 Score = 190 bits (483), Expect = 4e-53 Identities = 112/308 (36%), Positives = 178/308 (57%), Gaps = 18/308 (5%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L + NL V N + AV+ ++ V GE+LG++GESGSGK+ + A++ I PG Sbjct: 4 LLTIRNLAV-----NFNGLPAVDRINLDVAPGEVLGVVGESGSGKSVTMMALMGLIDAPG 58 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLP----ISEIF-YHEA 159 K+ + ++ FNG D+ + E RK++ KDI+ V Q + +LNP I E+ HE Sbjct: 59 KVTADEITFNGRDLLKASAKERRKIIGKDIAMVFQDALTSLNPSYTVGYQIKEVLKLHEG 118 Query: 160 ISHGEADKKRVIERASELLKLVGLDPARV-LKMYPFQLSGGMKQRVMIALSLLLNPKLIL 218 + DK RA ELL VG+ A+ + +P Q+SGGM QRVMIA+++ NPKL++ Sbjct: 119 LRGAALDK-----RALELLDQVGIPDAKSRIGAFPHQMSGGMNQRVMIAMAIACNPKLLI 173 Query: 219 MDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEG 278 DEPT+ALD+ Q +++L+ + +E G+ +V ++HD+ ++++A R+ VMY G V+E Sbjct: 174 ADEPTTALDVTIQAQIMELLMRLQKERGMALVLISHDLAVVSEVAQRVAVMYAGEVIETN 233 Query: 279 KTEEIIKSPLNPYTSLLVSSIPSLK-GEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGR 336 K +I +P +PYT L+++IP G V++ +P P + KGC F RC Sbjct: 234 KVPDIFAAPHHPYTEALLAAIPEHNVGAVRLAALPGMVPGRDDRPKGCLFAPRCKYMVDD 293 Query: 337 CKEELPEI 344 C P + Sbjct: 294 CNRGRPAL 301 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: 297 Number of extensions: 18 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: 362 Length of database: 334 Length adjustment: 29 Effective length of query: 333 Effective length of database: 305 Effective search space: 101565 Effective search space used: 101565 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: 49 (23.5 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