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 GFF2021 Psest_2064 ABC-type uncharacterized transport system, duplicated ATPase component
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__psRCH2:GFF2021 Length = 553 Score = 159 bits (403), Expect = 9e-44 Identities = 89/235 (37%), Positives = 144/235 (61%), Gaps = 6/235 (2%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE 82 I+AV V+F + + + + +VGESGSGK+T ILRLL + GEI F+G+ + + Sbjct: 303 IKAVDGVNFSLPKGQTLGIVGESGSGKSTLGLAILRLLG-SRGEIRFQGQHLQS--MSQR 359 Query: 83 SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGI 142 + RR++ VFQDPF S +P V + + + + + ++ N KE + I E+L VG+ Sbjct: 360 QVRPLRRQMQVVFQDPFGSLSPRMSVGQIVGEGLHI--HRMGNAKEQEQAIIEALVEVGL 417 Query: 143 DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELRE 202 DP + +YPH+ SGGQ+QRI IAR +L+P LI+ DEPTS +D + + +++LL L+ Sbjct: 418 DP-ETRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPTSALDRTVQRQVVELLRSLQA 476 Query: 203 EQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGS 257 + + +FI+HDL + +S + V+K G++VE+G + P H YT+ L+ S Sbjct: 477 KYNLTYLFISHDLAVVRALSHQMMVVKQGQVVEQGAAADIFAAPQHPYTQQLLES 531 Score = 152 bits (383), Expect = 2e-41 Identities = 91/265 (34%), Positives = 158/265 (59%), Gaps = 14/265 (5%) Query: 5 VVKNLTKIFSLG--FFSKRRIE-AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP 61 + +NL ++ L F + +++ V+ V+F++++ E ++LVGESGSGK+ TA ILRLLP Sbjct: 6 IAENLVEVRDLAVEFVTGEQVQRVVEGVTFDIRKGETLALVGESGSGKSVTAHSILRLLP 65 Query: 62 -----PTSGEIYFEGKDIWKDIKDRESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQA 115 G+I F G+D+ K D +++ + R ++ VFQ+P S NP + V + + + Sbjct: 66 YPLARHPQGQILFHGQDLLK--ADEKAMRKIRGNRIAMVFQEPMTSLNPLHTVGKQINEV 123 Query: 116 ISLLENKPSNKKEALELIKESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPL 174 + + +K K A E L VGI +P+ + YPH++SGGQ+QR++IA P Sbjct: 124 LEI--HKGLRGKAATARTLELLELVGIPEPRKRIRAYPHELSGGQRQRVVIAMALANEPE 181 Query: 175 LIVADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIV 234 L++ADEPT+ +D + + I++LL+EL+ G +++ I+HDL L ++ + VM+ G +V Sbjct: 182 LLIADEPTTALDVTVQLKILELLKELQARLGMALLLISHDLNLVRRIAHRVCVMQRGRVV 241 Query: 235 ERGHPDKVVLEPTHEYTKLLVGSIP 259 E+ + + P H YT+ L+ + P Sbjct: 242 EQALCEDLFRAPQHPYTQELLAAEP 266 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: 399 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 268 Length of database: 553 Length adjustment: 30 Effective length of query: 238 Effective length of database: 523 Effective search space: 124474 Effective search space used: 124474 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: 50 (23.9 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