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 Ac3H11_694 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_694 Length = 341 Score = 192 bits (487), Expect = 1e-53 Identities = 111/320 (34%), Positives = 181/320 (56%), Gaps = 9/320 (2%) Query: 5 LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64 LL+ ++R ++ V+AVD +SF I E +G+VGESG GK+T+ ++ +V P + Sbjct: 20 LLEIAHLRKHFGSGPHPVRAVDDVSFTIHRGETLGLVGESGSGKSTIGRLL-TRLVDPTS 78 Query: 65 LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAE 124 G++ +L+ +++ + + +I II Q +L P +R+ + + Sbjct: 79 ---GQMRYHGGAAPQDLAQLSQSQYRPL--RSQIQIIFQDPYASLNPRMRIRDVLAEALD 133 Query: 125 SHGIDEEEL-LDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADE 183 +HG+ + L + + E+VGL P +R+P E SGG RQR IA A + P ++ADE Sbjct: 134 THGLAKGAARLPRIHQLLEQVGLRPEHAERFPHEFSGGQRQRIGIARALAVEPQFIVADE 193 Query: 184 PTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPV 243 P SALDV Q ++ +L ++K Q + +++FI+HD+ V + DR++++Y G+++E AP Sbjct: 194 PLSALDVSIQAQVVNLLGELKEQ-LGLTLLFISHDLDVVEYLCDRVVVLYLGRVMEIAPT 252 Query: 244 ESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDV 303 E+L +P HPYTQ L + P+P ++R I + G P+ NPPSGC F RCP A Sbjct: 253 EALYAQPQHPYTQALLAAAPIPDP-AQRRSIALLQGDLPSPANPPSGCVFRTRCPQAEAR 311 Query: 304 CKEKEPPLTEIEPGRRVACW 323 C + L E+ PG ACW Sbjct: 312 CASADMQLREVAPGHLHACW 331 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: 270 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: 330 Length of database: 341 Length adjustment: 28 Effective length of query: 302 Effective length of database: 313 Effective search space: 94526 Effective search space used: 94526 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