Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Pf6N2E2_3425 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3425 Length = 328 Score = 175 bits (443), Expect = 2e-48 Identities = 102/316 (32%), Positives = 176/316 (55%), Gaps = 6/316 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L V +L+VI G + V+ VSF + KGEILG++GESGSGKT A++R + Sbjct: 5 VLHVEDLSVIAGHGEDEVT-LVDRVSFDLAKGEILGLVGESGSGKTMACRALMRLLPSAN 63 Query: 105 KIISGKVI-FNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163 + GK + G D+ S+ R + + + + Q + L+P++ I E H Sbjct: 64 LRVQGKALRLAGEDLLSLDEAGMRGIRGRRLGMIFQNPGSHLDPLMRIGEQIGEGIRLHQ 123 Query: 164 EADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 A K+ +A ++L+ VG+ DP + YP + SGGM+QR MIA++L NP++++ DEP Sbjct: 124 GASKREARAKAIDVLRQVGIPDPLTRVDSYPHEFSGGMRQRAMIAVALGCNPQVLIADEP 183 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 T+ALD+ Q +L+L+ ++ + G++I+ +THD+ +AQ + + VMY G + E G + Sbjct: 184 TTALDVTVQAQILRLLLDLRDQRGLSIIMITHDLGIVAQTCDSIAVMYAGRLCEHGNKLD 243 Query: 283 IIKSPLNPYTSLLVSSIPSLKGEVKVINVPLDEP--LVSKEKGCPFLARCSKAFGRCKEE 340 ++ P +PYT+ L+ P+ ++ +P L + GC F RC + +C Sbjct: 244 LLAHPRHPYTAALIDCQPATSAGHAMLKTIAGQPPLLDALPSGCRFNPRCLQQGSQCTRL 303 Query: 341 LPEIRLVYD-RKVRCH 355 LP++++ + +V CH Sbjct: 304 LPQMQVTAEAHRVACH 319 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: 224 Number of extensions: 7 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: 328 Length adjustment: 29 Effective length of query: 333 Effective length of database: 299 Effective search space: 99567 Effective search space used: 99567 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