Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate RR42_RS10815 RR42_RS10815 methionine ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Cup4G11:RR42_RS10815 Length = 336 Score = 202 bits (514), Expect = 1e-56 Identities = 115/316 (36%), Positives = 187/316 (59%), Gaps = 6/316 (1%) Query: 43 VMILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRP 102 V LEV +L + E + ++ AV+DVSF V +G ILG++GESGSGK+ +I+ + P Sbjct: 10 VPTLEVRHLRTHF-ETRAGVLPAVDDVSFTVPRGRILGLVGESGSGKSVTGFSIMGLVDP 68 Query: 103 PGKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISH 162 PG+I G+++F G ++ M E R+L I+ + Q LNPV+ + +H Sbjct: 69 PGRIAGGEILFQGRELTRMRPAELRQLQGNRIAMIFQDPMMTLNPVMRVDAQMIEAVRAH 128 Query: 163 GEADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDE 221 A K+ E A + L ++G+ P L+ YP QLSGGM+QRV IA+++L P LI+ DE Sbjct: 129 SPASHKQARELARDTLGMMGIPSPEERLRAYPHQLSGGMRQRVAIAIAMLHRPDLIIADE 188 Query: 222 PTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTE 281 PT+ALD+ Q +L ++ + + G ++++THD+ +A +A+ + VMY G ++E+G + Sbjct: 189 PTTALDVTIQAQILSEVQKLARLHGTALIWITHDLSVVAGLADEVAVMYAGRIVEQGPVD 248 Query: 282 EIIKSPLNPYTSLLVSSIPSL--KGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCK 338 ++ PL+PYT+ L+ S+PSL +G+ ++ +P P L++ GC F ARC + G C Sbjct: 249 AVLDHPLHPYTAGLIGSLPSLNQRGQ-RLRQIPGMTPNLLTMPPGCAFAARCPRVSGACV 307 Query: 339 EELPEIRLVYDRKVRC 354 + R+VRC Sbjct: 308 QAPAITSPQALRQVRC 323 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: 241 Number of extensions: 9 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: 336 Length adjustment: 29 Effective length of query: 333 Effective length of database: 307 Effective search space: 102231 Effective search space used: 102231 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