Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate PP_4150 PP_4150 microcin C transporter - ATP binding subunit
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Putida:PP_4150 Length = 534 Score = 229 bits (584), Expect = 1e-64 Identities = 122/255 (47%), Positives = 174/255 (68%), Gaps = 1/255 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN-G 62 L+ V +L VEF + + + VDG+S+ + KGE+L +VGESGSGKSV+ S+LRL+ Sbjct: 6 LIEVRDLAVEFVTGDQVNRVVDGVSFDIRKGETLALVGESGSGKSVTAHSILRLLPYPLA 65 Query: 63 RIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122 R G + GKDLL+ +++ L+ IRG I++IFQ PMTSLNP+ + Q+ E ++ H+ Sbjct: 66 RHPSGSIRYEGKDLLQQSEKTLQRIRGNRIAMIFQEPMTSLNPLHCIEKQINEILLLHKG 125 Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 + +EA R +ELL+ VGIPE KR P + SGG RQRVMIAMALA P+LLIADEPT Sbjct: 126 LTGKEATARTLELLDMVGIPEPRKRLKALPHELSGGQRQRVMIAMALANEPELLIADEPT 185 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 TALDVT+Q +I+ELL+EL+ GM+++ I+HDL++ R+ M G+IVE+A + Sbjct: 186 TALDVTVQLKILELLKELQARMGMALLLISHDLNLVRRIAHRVCVMQRGQIVEQAECATL 245 Query: 243 LKTPLHPYTKGLLNS 257 +P H YT+ L+N+ Sbjct: 246 FSSPQHHYTQMLINA 260 Score = 187 bits (475), Expect = 5e-52 Identities = 110/267 (41%), Positives = 168/267 (62%), Gaps = 16/267 (5%) Query: 4 LLNVNNLKVEFHRVEGI-------VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56 LL V++LKV F +G VKAVDG+++ L +G++LGIVGESGSGKS L++LR Sbjct: 275 LLEVDDLKVWFPIKKGFLQRTVDHVKAVDGVNFSLPQGQTLGIVGESGSGKSTLGLAILR 334 Query: 57 LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116 LI+ G I F G++L LN++ +R +R +++ ++FQ+P SL+P + V V E Sbjct: 335 LISSQGGIR-----FHGQNLEGLNQKAVRPLR-REMQVVFQDPFGSLSPRMCVADIVGEG 388 Query: 117 IIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLL 176 + HR+ +E I LE VG+ P+ YP +FSGG RQR+ IA AL P L+ Sbjct: 389 LRIHRIGTAQEQEAAIIAALEEVGL--DPRTRHRYPHEFSGGQRQRIAIARALVLKPALI 446 Query: 177 IADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236 + DEPT+ALD T+Q Q++ELL+ L+++Y ++ +FI+HDL+V +++ + G +VE+ Sbjct: 447 LLDEPTSALDRTVQRQVVELLRNLQQKYNLTYLFISHDLAVVKALSHQLMVIKHGHVVEQ 506 Query: 237 APVEEILKTPLHPYTKGLLNST-LEIG 262 + I P HPYT+ LL + LE+G Sbjct: 507 GDAQAIFHAPQHPYTRQLLEAAFLEVG 533 Lambda K H 0.320 0.139 0.401 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: 454 Number of extensions: 19 Number of successful extensions: 5 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: 324 Length of database: 534 Length adjustment: 31 Effective length of query: 293 Effective length of database: 503 Effective search space: 147379 Effective search space used: 147379 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: 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