Align TM0027, 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 Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 100 bits (250), Expect = 2e-26 Identities = 73/238 (30%), Positives = 126/238 (52%), Gaps = 14/238 (5%) Query: 1 MSRLVVKNLTKIFSLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60 M L ++N++KI+ G R + +++++ VK + +++VG SGSGKTT + L Sbjct: 1 MDILSIENVSKIYQSG---SRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLD 57 Query: 61 PPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLE 120 +SG + G + +D+ + V +++ +FQ+ P L + LE Sbjct: 58 SASSGSVALNGHRLEGLSEDQRAAVR-SQEIGFIFQN-----FQLLPTLTALENVMVPLE 111 Query: 121 NKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADE 180 K +K+A + E L +VG+ D + YP Q+SGG++QR+ IAR + P ++ ADE Sbjct: 112 LK--KRKDAKQKATELLQQVGLG--DRMTHYPTQLSGGEQQRVSIARAFANEPKILFADE 167 Query: 181 PTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGH 238 PT +D + I L+ +L + GT++I +THD LA ++ I +K G+I E H Sbjct: 168 PTGNLDTETGELIETLIFDLNKALGTTLILVTHDTDLA-AKTNRIIHIKGGKIQEEQH 224 Lambda K H 0.319 0.139 0.397 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: 144 Number of extensions: 12 Number of successful extensions: 2 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: 268 Length of database: 225 Length adjustment: 24 Effective length of query: 244 Effective length of database: 201 Effective search space: 49044 Effective search space used: 49044 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 (21.7 bits) S2: 46 (22.3 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