Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF1853 HP15_1810 peptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Marino:GFF1853 Length = 534 Score = 226 bits (577), Expect = 8e-64 Identities = 122/266 (45%), Positives = 169/266 (63%), Gaps = 11/266 (4%) Query: 1 MPFDQGGIKMKPLLQTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESG 53 +P D+ + +PLL L FP K +L AV G ++ GETLG+VGESG Sbjct: 262 LPLDK---RAEPLLAVERLDVRFPIRKSLLGKVKESFHAVQGADFQLNRGETLGIVGESG 318 Query: 54 CGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTV 113 GK+T+G +LKL G I G+++ LN K+ +P+R+++QI+FQDP GSL+P+M++ Sbjct: 319 SGKTTIGHALLKLTASTGS-IRLRGEELAFLNQKDFRPWRRRVQIVFQDPFGSLSPRMSI 377 Query: 114 GRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALAL 173 II + L IH E +V L VG+ E + +PHEFSGGQ+QRI IARAL L Sbjct: 378 AEIIREGLEIHDAENAAEHDSKVIRALTDVGLDPEARHRYPHEFSGGQRQRIAIARALVL 437 Query: 174 NPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLG 233 P I+ DEP SALD ++Q Q+I+LL IQ + G+SY+FI+H+LAVV +SHK+ V+ G Sbjct: 438 QPDLIILDEPTSALDRTVQKQVIELLRAIQTRYGLSYIFISHDLAVVRALSHKLLVLQHG 497 Query: 234 KIVEYGDVDKIFLNPIHPYTRALLKS 259 +IVEYGD +IF P YTR LL + Sbjct: 498 RIVEYGDAARIFAAPQAEYTRELLNA 523 Score = 192 bits (489), Expect = 1e-53 Identities = 110/260 (42%), Positives = 162/260 (62%), Gaps = 11/260 (4%) Query: 10 MKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRP 69 M LLQ DL F G AV+ +S+ I+EGETL LVGESG GKS +IL+LL Sbjct: 1 MSQLLQISDLSICFDHGP---PAVESLSLAIREGETLALVGESGSGKSISALSILRLLDA 57 Query: 70 -----DGGKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLII 123 G+I + +D+ +K M+ R +++ +IFQ+P+ SLNP TV + I + L + Sbjct: 58 RHASYPSGQIRYRDEDLLAATEKRMRQIRGREIGMIFQEPMTSLNPLHTVEKQIGETLEL 117 Query: 124 HKIGTKKERRKRVEELLDMVGIGR--EFINSFPHEFSGGQQQRIGIARALALNPKFIVCD 181 HK + ++R ELL +VGI + ++PH+ SGGQ+QR+ IA ALA P ++ D Sbjct: 118 HKGMRGPQAKQRCLELLQLVGIQNPESKLGAYPHQLSGGQKQRVMIAMALANEPDLLIAD 177 Query: 182 EPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDV 241 EP +ALDV++Q Q+++LL ++Q+K+G++ L I H+L +V + VAVM GK+VE D Sbjct: 178 EPTTALDVTVQKQVLELLRDLQKKLGMAILLITHDLTIVRRYADHVAVMEHGKLVEEADT 237 Query: 242 DKIFLNPIHPYTRALLKSVP 261 D +F +P HPYTR LL + P Sbjct: 238 DALFASPQHPYTRKLLDAEP 257 Lambda K H 0.321 0.142 0.417 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: 491 Number of extensions: 27 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: 328 Length of database: 534 Length adjustment: 32 Effective length of query: 296 Effective length of database: 502 Effective search space: 148592 Effective search space used: 148592 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