Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 17602 b3541 dipeptide transporter (NCBI)
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Keio:17602 Length = 327 Score = 198 bits (503), Expect = 2e-55 Identities = 111/315 (35%), Positives = 188/315 (59%), Gaps = 5/315 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L V L+V + + S +AV+ +S+ V++GE++GI+GESGSGK+ AI+ I PG Sbjct: 3 LLNVDKLSVHFGD-ESAPFRAVDRISYSVKQGEVVGIVGESGSGKSVSSLAIMGLIDYPG 61 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 ++++ K+ FNG D+ ++ E R L+ +++ + Q +LNP + H Sbjct: 62 RVMAEKLEFNGQDLQRISEKERRNLVGAEVAMIFQDPMTSLNPCYTVGFQIMEAIKVHQG 121 Query: 165 ADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPT 223 +K +RA +LL VG+ DPA L +YP QLSGGM QRVMIA+++ PKL++ DEPT Sbjct: 122 GNKSTRRQRAIDLLNQVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACRPKLLIADEPT 181 Query: 224 SALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEI 283 +ALD+ Q +++L+ + Q+ + +V +THD+ +A+ A++++VMY G V+E G I Sbjct: 182 TALDVTIQAQIIELLLELQQKENMALVLITHDLALVAEAAHKIIVMYAGQVVETGDAHAI 241 Query: 284 IKSPLNPYTSLLVSSIPSL-KGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEEL 341 +P +PYT L+ ++P + + ++ ++P P + GC RC A RC+ E Sbjct: 242 FHAPRHPYTQALLRALPEFAQDKERLASLPGVVPGKYDRPNGCLLNPRCPYATDRCRAEE 301 Query: 342 PEIRLVYD-RKVRCH 355 P + ++ D R+ +CH Sbjct: 302 PALNMLADGRQSKCH 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: 285 Number of extensions: 12 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: 327 Length adjustment: 29 Effective length of query: 333 Effective length of database: 298 Effective search space: 99234 Effective search space used: 99234 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