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 PfGW456L13_5057 Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5057 Length = 322 Score = 164 bits (415), Expect = 3e-45 Identities = 107/324 (33%), Positives = 178/324 (54%), Gaps = 36/324 (11%) Query: 5 LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64 LL+ +N+ + +K + VDGL ++ + EV+ +VGESG GK+ ++ + M +++ Sbjct: 3 LLEIKNLNVRFG-DKNATPVVDGLDLQVDKGEVLAIVGESGSGKS-VTMMALMGLIEHPG 60 Query: 65 LV-------DGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPT----I 113 +V DGK L++N + +R+ GK+++++ Q M AL P+ Sbjct: 61 IVTADALNFDGKNMLKLN-----------NRQRRQIVGKDLSMVFQDPMTALNPSYTVGF 109 Query: 114 RMEKYVR-HLAESHGIDEE---ELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIA 169 ++E+ +R HL S + ELL+K +D YP +LSGGM QR IA Sbjct: 110 QIEEVLRLHLKMSGKAARKRAIELLEKVEIPGAASRMDA-----YPHQLSGGMSQRVAIA 164 Query: 170 IATILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRM 229 +A P LLIADEPT+ALDV Q ++ +L+ ++++ + ++ ITHD+A V + A R+ Sbjct: 165 MAIAGEPKLLIADEPTTALDVTIQAQIMDLLLALQKEQNM-GLVLITHDLAVVAETAQRV 223 Query: 230 IIMYAGKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPS 289 +MYAG+ VE V L + P HPY++ L ++ PE + ++T+PG P + P Sbjct: 224 CVMYAGQAVEVGQVPQLFDIPAHPYSEALLKAI--PEHSLGASRLSTLPGIVPGRYDRPQ 281 Query: 290 GCRFHPRCPHAMDVCKEKEPPLTE 313 GC PRCP+ D C+++ P L + Sbjct: 282 GCLLSPRCPYVKDNCRQQRPALDQ 305 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: 278 Number of extensions: 14 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: 322 Length adjustment: 28 Effective length of query: 302 Effective length of database: 294 Effective search space: 88788 Effective search space used: 88788 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: 48 (23.1 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