Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate 8500263 DvMF_1020 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Miya:8500263 Length = 358 Score = 186 bits (472), Expect = 8e-52 Identities = 114/324 (35%), Positives = 173/324 (53%), Gaps = 22/324 (6%) Query: 22 VKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVEL 81 ++AV G+SF I + +VGESGCGK+ + + + +P + G + R+ G EL Sbjct: 41 LRAVAGISFSIAPGGTLCLVGESGCGKSMTALALLRLVPEPGRVASGSV--RLEGR--EL 96 Query: 82 SSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESH-GIDEEELLDKARRR 140 ++ E+ R G+ I++I Q M +L P R+ + + H G+ + +A Sbjct: 97 LTLPEPEM-RGVRGRSISMIFQEPMTSLNPVFRVGEQIAEGVRLHLGLSRSDAAARAVDL 155 Query: 141 FEEVGLDP--LWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLK 198 +VG+ L + +P ++SGGMRQR +IA+A +P LLIADEPT+ALDV Q+ +L+ Sbjct: 156 LRQVGIPSPELRARDFPHQMSGGMRQRVMIAMALACDPRLLIADEPTTALDVTIQRQILR 215 Query: 199 VLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGL 258 ++ + S++ ITHD+ V + AD + +MYAG+I+E A V +PLHPY QGL Sbjct: 216 LMRDLAAHRGA-SVLLITHDLGVVAETADHVAVMYAGRIMEHASVGDFFARPLHPYAQGL 274 Query: 259 FNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEP-- 316 SV + ++ IPG P L PSGC F RCPHA C E+EPPL + P Sbjct: 275 MRSVPQAVSGPRAERLSAIPGTVPPLWALPSGCTFRDRCPHAFARCAEQEPPLLAMPPQA 334 Query: 317 -----------GRRVACWLYMEER 329 V CWL+ ++ Sbjct: 335 LAATPTDNAAQAHGVRCWLHAPKK 358 Lambda K H 0.321 0.138 0.405 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: 316 Number of extensions: 13 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: 330 Length of database: 358 Length adjustment: 29 Effective length of query: 301 Effective length of database: 329 Effective search space: 99029 Effective search space used: 99029 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