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 PP_4150 PP_4150 microcin C transporter - ATP binding subunit
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Putida:PP_4150 Length = 534 Score = 159 bits (402), Expect = 1e-43 Identities = 93/241 (38%), Positives = 147/241 (60%), Gaps = 11/241 (4%) Query: 26 VKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLP-----PTSGEIYFEGKDIWKDIKD 80 V VSF++++ E ++LVGESGSGK+ TA ILRLLP SG I +EGKD+ + + Sbjct: 26 VDGVSFDIRKGETLALVGESGSGKSVTAHSILRLLPYPLARHPSGSIRYEGKDLLQ--QS 83 Query: 81 RESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFR 139 ++L R ++ +FQ+P S NP + +E+ + + LL +K KEA E L Sbjct: 84 EKTLQRIRGNRIAMIFQEPMTSLNPLHCIEKQINEI--LLLHKGLTGKEATARTLELLDM 141 Query: 140 VGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLE 198 VGI +P+ L PH++SGGQ+QR+MIA P L++ADEPT+ +D + + I++LL+ Sbjct: 142 VGIPEPRKRLKALPHELSGGQRQRVMIAMALANEPELLIADEPTTALDVTVQLKILELLK 201 Query: 199 ELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSI 258 EL+ G +++ I+HDL L ++ + VM+ G+IVE+ + P H YT++L+ + Sbjct: 202 ELQARMGMALLLISHDLNLVRRIAHRVCVMQRGQIVEQAECATLFSSPQHHYTQMLINAE 261 Query: 259 P 259 P Sbjct: 262 P 262 Score = 150 bits (378), Expect = 7e-41 Identities = 83/233 (35%), Positives = 144/233 (61%), Gaps = 6/233 (2%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE 82 ++AV V+F + + + + +VGESGSGK+T ILRL+ + G I F G+++ + +++ Sbjct: 299 VKAVDGVNFSLPQGQTLGIVGESGSGKSTLGLAILRLIS-SQGGIRFHGQNL--EGLNQK 355 Query: 83 SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGI 142 ++ RR++ VFQDPF S +P V + + + + + ++EA I +L VG+ Sbjct: 356 AVRPLRREMQVVFQDPFGSLSPRMCVADIVGEGLRIHRIGTAQEQEAA--IIAALEEVGL 413 Query: 143 DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELRE 202 DP+ +YPH+ SGGQ+QRI IAR +L+P LI+ DEPTS +D + + +++LL L++ Sbjct: 414 DPR-TRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPTSALDRTVQRQVVELLRNLQQ 472 Query: 203 EQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLV 255 + + +FI+HDL + +S + V+K+G +VE+G + P H YT+ L+ Sbjct: 473 KYNLTYLFISHDLAVVKALSHQLMVIKHGHVVEQGDAQAIFHAPQHPYTRQLL 525 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: 367 Number of extensions: 23 Number of successful extensions: 6 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: 534 Length adjustment: 30 Effective length of query: 238 Effective length of database: 504 Effective search space: 119952 Effective search space used: 119952 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