Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate H281DRAFT_03126 H281DRAFT_03126 oligopeptide transport system ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Burk376:H281DRAFT_03126 Length = 333 Score = 179 bits (455), Expect = 7e-50 Identities = 101/306 (33%), Positives = 172/306 (56%), Gaps = 7/306 (2%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +LEV +L+V + + AV VSF +E G LGI+GESGSGK+ + A+L + G Sbjct: 3 LLEVKDLSVRFTRREGAPVDAVQRVSFSLEPGRTLGIVGESGSGKSQTVMALLGLLAGNG 62 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 + SG+ ++ G ++ +M K+ I + Q +LNP L I H + Sbjct: 63 NV-SGEALYRGENLLAMNEAALNKIRGDRIGMIFQDPMTSLNPFLTIERQMTETLQLHRK 121 Query: 165 ADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 ++ RA E L+ V + D AR + MYP + SGGM+QRVMIA++LL P++++ DEPT Sbjct: 122 MSRRDARRRAIETLETVRIPDSARRIGMYPHEFSGGMRQRVMIAMALLSEPEILIADEPT 181 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q +++L++ +N+E G I+ +THD+ +A + + ++VMY G +E+ + Sbjct: 182 TALDVTVQAQIIELLRELNRERGTAIILITHDMGVVAGLCDDVMVMYAGQTVEQASAASL 241 Query: 284 IKSPLNPYTSLLVSSIPSL----KGEVKVINVPLDEPLVSK-EKGCPFLARCSKAFGRCK 338 +P +PYT L++++P L + + +P + PL + GC F RC+ +C+ Sbjct: 242 FAAPTHPYTRGLLNALPRLTDSSDDDRPLQTIPGNPPLPGEVGAGCAFAPRCAYCSDQCR 301 Query: 339 EELPEI 344 + P + Sbjct: 302 QSRPAL 307 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: 240 Number of extensions: 12 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: 333 Length adjustment: 29 Effective length of query: 333 Effective length of database: 304 Effective search space: 101232 Effective search space used: 101232 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