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 GFF2386 PS417_12165 microcin ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__WCS417:GFF2386 Length = 523 Score = 228 bits (580), Expect = 3e-64 Identities = 121/251 (48%), Positives = 174/251 (69%), Gaps = 7/251 (2%) Query: 13 LLQTVDLKKYFPQG------KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKL 66 +LQ DL F G K L+AVDGIS+ ++ G+TLG+VGESG GKSTLG+ IL+L Sbjct: 267 VLQVDDLTVQFRLGGGLFRRKTYLRAVDGISLSVQRGKTLGIVGESGSGKSTLGQAILRL 326 Query: 67 LRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126 L G I F+G+ + LN+++M+P+RK+MQ++FQDP GSL+P+MTV +II + L +H Sbjct: 327 L-DSTGSIRFQGEALDPLNNQQMRPWRKQMQVVFQDPYGSLSPRMTVEQIISEGLEVHAP 385 Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186 + +R +V ++L VG+ + +PHEFSGGQ+QRI IARAL L P ++ DEP SA Sbjct: 386 CSLADRDAQVIQVLKDVGLDPASRHRYPHEFSGGQRQRIAIARALVLKPALMLLDEPTSA 445 Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246 LD ++Q Q++ LL E+Q K G++YLFI+H+LAVV ++H + V+ G++VE G +F Sbjct: 446 LDRTVQKQVVALLRELQDKYGLTYLFISHDLAVVRAMAHDMIVIKDGQVVERGASHAVFD 505 Query: 247 NPIHPYTRALL 257 P HPYT+ LL Sbjct: 506 APQHPYTKELL 516 Score = 178 bits (451), Expect = 3e-49 Identities = 96/236 (40%), Positives = 154/236 (65%), Gaps = 7/236 (2%) Query: 33 VDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG----GKIFFEGKDITNLNDKE 88 V +S++++ GE L LVGESG GKS +IL+LL G G I + G+++ + Sbjct: 19 VRNLSLDVRPGECLALVGESGSGKSVTAHSILQLLPEAGTETTGSIQYRGQELIGASAAT 78 Query: 89 MKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGR 147 ++ R ++ +IFQ+P+ SLNP ++ + I + L++HK K + R+ ELLD+VGI + Sbjct: 79 LQKLRGNRIAMIFQEPMTSLNPLHSIEKQIGETLLLHKGLGGKAAQARILELLDLVGIQK 138 Query: 148 --EFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQK 205 E + ++PH+ SGGQ+QR+ IA ALA P+ ++ DEP +ALDV++Q +I+ LL+ +Q++ Sbjct: 139 PQERLKAYPHQLSGGQRQRVMIAMALACEPELLIADEPTTALDVTVQRKILLLLKSLQKR 198 Query: 206 MGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVP 261 +G+S L I+H+L +V I+ +V VM G+IVE D +F P HPY+R LL + P Sbjct: 199 LGMSLLLISHDLNLVRSIAQRVCVMRAGEIVEQADCQTLFNAPQHPYSRLLLDAEP 254 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: 502 Number of extensions: 20 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: 523 Length adjustment: 31 Effective length of query: 297 Effective length of database: 492 Effective search space: 146124 Effective search space used: 146124 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