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 GFF1853 HP15_1810 peptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Marino:GFF1853 Length = 534 Score = 231 bits (588), Expect = 4e-65 Identities = 118/258 (45%), Positives = 177/258 (68%), Gaps = 4/258 (1%) Query: 1 MMELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLIN- 59 M +LL +++L + F AV+ +S + +GE+L +VGESGSGKS+S LS+LRL++ Sbjct: 1 MSQLLQISDLSICFDHGP---PAVESLSLAIREGETLALVGESGSGKSISALSILRLLDA 57 Query: 60 RNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIW 119 R+ G+ + +DLL ++ +R IRG++I +IFQ PMTSLNP+ V Q+ E + Sbjct: 58 RHASYPSGQIRYRDEDLLAATEKRMRQIRGREIGMIFQEPMTSLNPLHTVEKQIGETLEL 117 Query: 120 HRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIAD 179 H+ M+ +A++R +ELL+ VGI + YP Q SGG +QRVMIAMALA P LLIAD Sbjct: 118 HKGMRGPQAKQRCLELLQLVGIQNPESKLGAYPHQLSGGQKQRVMIAMALANEPDLLIAD 177 Query: 180 EPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPV 239 EPTTALDVT+Q Q++ELL++L+++ GM+++ ITHDL++ + D + M GK+VEEA Sbjct: 178 EPTTALDVTVQKQVLELLRDLQKKLGMAILLITHDLTIVRRYADHVAVMEHGKLVEEADT 237 Query: 240 EEILKTPLHPYTKGLLNS 257 + + +P HPYT+ LL++ Sbjct: 238 DALFASPQHPYTRKLLDA 255 Score = 163 bits (412), Expect = 1e-44 Identities = 103/262 (39%), Positives = 149/262 (56%), Gaps = 17/262 (6%) Query: 4 LLNVNNLKVEFH-------RVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56 LL V L V F +V+ AV G ++LN+GE+LGIVGESGSGK+ +LL+ Sbjct: 271 LLAVERLDVRFPIRKSLLGKVKESFHAVQGADFQLNRGETLGIVGESGSGKTTIGHALLK 330 Query: 57 LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116 L G I G++L LN+++ R R + + I+FQ+P SL+P + + + E Sbjct: 331 LTASTGSIR-----LRGEELAFLNQKDFRPWRRR-VQIVFQDPFGSLSPRMSIAEIIREG 384 Query: 117 IIWHRLMKNEEARERAIELLERVGI-PESPKRFLNYPFQFSGGMRQRVMIAMALACHPKL 175 + H E + I L VG+ PE+ R YP +FSGG RQR+ IA AL P L Sbjct: 385 LEIHDAENAAEHDSKVIRALTDVGLDPEARHR---YPHEFSGGQRQRIAIARALVLQPDL 441 Query: 176 LIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVE 235 +I DEPT+ALD T+Q Q++ELL+ ++ YG+S IFI+HDL+V +++ + G+IVE Sbjct: 442 IILDEPTSALDRTVQKQVIELLRAIQTRYGLSYIFISHDLAVVRALSHKLLVLQHGRIVE 501 Query: 236 EAPVEEILKTPLHPYTKGLLNS 257 I P YT+ LLN+ Sbjct: 502 YGDAARIFAAPQAEYTRELLNA 523 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: 442 Number of extensions: 22 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