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 AO353_21785 AO353_21785 microcin ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21785 Length = 526 Score = 237 bits (605), Expect = 4e-67 Identities = 122/251 (48%), Positives = 176/251 (70%), Gaps = 7/251 (2%) Query: 13 LLQTVDLKKYFPQG------KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKL 66 +L+ DL FP G K L AVDGIS+ I+ G+TLG+VGESG GKSTLG+ IL+L Sbjct: 269 VLEVNDLNVRFPLGGGLFQRKTWLHAVDGISLSIQRGKTLGIVGESGSGKSTLGQAILRL 328 Query: 67 LRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126 L DG I F+G+ + +LN K+++P+RK+MQ++FQDP GSL+P+M+V +II + L +H Sbjct: 329 LDSDGS-IRFQGEALDSLNQKQLRPWRKQMQVVFQDPFGSLSPRMSVAQIISEGLEVHSQ 387 Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186 + E +V ++L VG+ + + +PHEFSGGQ+QRI IARAL L P I+ DEP SA Sbjct: 388 SSAAECETQVIQVLKEVGLDPQSRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPTSA 447 Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246 LD ++Q Q++ LL ++Q+K G++YLFI+H+LAV+ ++H + V+ GK+VE G +F Sbjct: 448 LDRTVQKQVVALLRQLQEKYGLTYLFISHDLAVIRALAHDMIVIKDGKVVERGASHDVFA 507 Query: 247 NPIHPYTRALL 257 P HPYT+ LL Sbjct: 508 APQHPYTKELL 518 Score = 187 bits (476), Expect = 4e-52 Identities = 100/239 (41%), Positives = 162/239 (67%), Gaps = 9/239 (3%) Query: 32 AVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGG-----KIFFEGKDITNLND 86 AV + ++I+ GE L LVGESG GKS ++IL+LL PDGG I + G+++ + Sbjct: 20 AVRNVCLDIRPGECLALVGESGSGKSVTAQSILQLL-PDGGTETRGSIRYRGQELIGADV 78 Query: 87 KEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGI 145 ++ R ++ +IFQ+P+ SLNP +V + I + L++HK K +KR ELL++VGI Sbjct: 79 ATLRALRGNRIAMIFQEPMTSLNPLHSVEKQIGETLLVHKGLGDKAAQKRTLELLELVGI 138 Query: 146 GR--EFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQ 203 + E + ++PH+ SGGQ+QR+ IA ALA P+ ++ DEP +ALDV++Q +I+ LL+ +Q Sbjct: 139 KKPEERLKAYPHQLSGGQRQRVMIAMALACEPELLIADEPTTALDVTVQRKILRLLKSLQ 198 Query: 204 QKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPK 262 Q++G+S L I+H+L +V I+ +V VM+ G+IVE + +++F +P HPY+R LL + P+ Sbjct: 199 QRLGMSLLLISHDLNLVRSIAQRVCVMHAGEIVEQAECERLFNHPQHPYSRLLLNAEPE 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: 507 Number of extensions: 14 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: 526 Length adjustment: 31 Effective length of query: 297 Effective length of database: 495 Effective search space: 147015 Effective search space used: 147015 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