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 GFF667 PGA1_c06810 putative dipeptide transport ATP-binding protein DppD
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Phaeo:GFF667 Length = 326 Score = 197 bits (501), Expect = 3e-55 Identities = 116/303 (38%), Positives = 176/303 (58%), Gaps = 12/303 (3%) Query: 24 AVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSS 83 A D +S++I E++GVVGESG GK+ N + + P + G+I R+NG+ ++ + Sbjct: 24 ATDKVSYDIAPGEILGVVGESGAGKSMAGNAVIGLLNPPARITGGEI--RLNGQRID--N 79 Query: 84 MTRDEVKRKFWGKEITIIPQAAMNALMPTIRM-EKYVRHLAESHGIDEEELLDKARRRFE 142 + R++++R GKEI +I Q + +L P +R+ ++ + E + + E +A E Sbjct: 80 LPREKMRR-LRGKEIGMIFQDPLTSLNPLLRIGDQLTETMMEHLELTKPEARARAIAALE 138 Query: 143 EVGLDPLW--IKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVL 200 EVG+ I YP E SGGMRQR VIA+A PSL+IADEPT+ALDV Q ++ +L Sbjct: 139 EVGIPAASERIDSYPHEFSGGMRQRVVIALALCAEPSLIIADEPTTALDVSVQAQIIALL 198 Query: 201 MQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGLFN 260 ++ R+ +++ ITHD+ + + ADR+ +MYAG++ E V ++ +P HPYT GL Sbjct: 199 KRLCRER-GTAVMLITHDMGVIAEAADRVAVMYAGRMAEIGDVRDVVTRPRHPYTDGLMG 257 Query: 261 SVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEPGRRV 320 S TP + + IPGA P L + P GC F PRC A + C+ PP E + GR Sbjct: 258 S--TPSASAGQHRLRQIPGAMPRLHSLPPGCAFSPRCERANERCRNSPPPTLEADNGRS- 314 Query: 321 ACW 323 ACW Sbjct: 315 ACW 317 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: 310 Number of extensions: 16 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: 326 Length adjustment: 28 Effective length of query: 302 Effective length of database: 298 Effective search space: 89996 Effective search space used: 89996 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