Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Pf1N1B4_1127 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1127 Length = 326 Score = 171 bits (433), Expect = 3e-47 Identities = 102/298 (34%), Positives = 163/298 (54%), Gaps = 13/298 (4%) Query: 63 IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122 ++A+N VSF +E G+ L ++GESG GK+TL A+ P SG + G ++ Sbjct: 27 VRALNGVSFELEAGKTLAVVGESGCGKSTLARALTLIEEPS----SGSLKIAGQEVAGAD 82 Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVG 182 + RK L KD+ V Q+ +LNP + + + + E+ ++K VG Sbjct: 83 KAQ-RKQLRKDVQMVFQSPYASLNPRQKVGDQLAEPLLINTNLSASERREKVQAMMKQVG 141 Query: 183 LDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNIN 242 L P + YP SGG +QR+ +A +++L PK+++ DEPTSALD+ Q +L L ++ Sbjct: 142 LRPEHYQR-YPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQAQVLNLFMDLQ 200 Query: 243 QEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSSIPSL 302 QE V+++H++ + +A+ ++VMY G +E G E+I PL+PYT L+S+ P++ Sbjct: 201 QEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGPKEDIYTRPLHPYTQALLSATPTI 260 Query: 303 -----KGEVKVINVPLDEPLVSKEKGCPFLARCSKAFGRCKEELPEIRLVYDRKVRCH 355 K ++K++ L PL + GC F RC A RC E P +RLV R+V CH Sbjct: 261 HPDPTKPKIKIVG-ELPNPL-NPPSGCAFHKRCPYATDRCTTEEPLLRLVDTRQVACH 316 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: 267 Number of extensions: 10 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: 362 Length of database: 326 Length adjustment: 29 Effective length of query: 333 Effective length of database: 297 Effective search space: 98901 Effective search space used: 98901 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 Apr 09 2024. 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