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 3607471 Dshi_0884 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Dino:3607471 Length = 360 Score = 193 bits (491), Expect = 5e-54 Identities = 117/330 (35%), Positives = 179/330 (54%), Gaps = 13/330 (3%) Query: 1 MKEILLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMV 60 M + +L N+ ++ VD +S++I E++GVVGESG GK+ N + + Sbjct: 1 MTQPVLSIRNLTVDIPTRYAVLRPVDKVSYDIAPGEILGVVGESGAGKSMAGNAVIGLLT 60 Query: 61 KPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVR 120 P + G+++L NG+ ++ + E R+ GK+I ++ Q + +L P +R+ + Sbjct: 61 PPAHISSGEVWL--NGKRIDRLT---PEQMRRVRGKDIGMVFQDPLTSLNPLLRIGDQLT 115 Query: 121 HLAESH-GIDEEELLDKARRRFEEVGLDPLW--IKRYPFELSGGMRQRAVIAIATILNPS 177 +H I E ++A EEVG+ + YP E SGGMRQR VIA+A PS Sbjct: 116 ETMLAHLPISRAEAEERAVAALEEVGIPAARQRVNSYPHEFSGGMRQRVVIALALCAEPS 175 Query: 178 LLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237 L+IADEPT+ALDV Q ++ +L ++ R+ +++ ITHD+ + + ADR+ +MYAG++ Sbjct: 176 LVIADEPTTALDVSVQAQIIALLKRLCRER-GTAVMLITHDMGVIAEAADRVAVMYAGRL 234 Query: 238 VEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRC 297 E PV +L P HPYT GL S TP + + IPG+ P L P GC F PRC Sbjct: 235 AELGPVREVLTAPRHPYTFGLMGS--TPLASKGLKRLHQIPGSMPRLGRLPPGCAFSPRC 292 Query: 298 PHAMDVCKEKEPPLTEIEPGRRVACWLYME 327 P A D C+ P+ I+ ACW M+ Sbjct: 293 PRAQDKCRHDPGPV--IDADGAAACWFPMD 320 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: 337 Number of extensions: 20 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: 360 Length adjustment: 29 Effective length of query: 301 Effective length of database: 331 Effective search space: 99631 Effective search space used: 99631 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