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 WP_086508118.1 BZY95_RS00870 ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >NCBI__GCF_002151265.1:WP_086508118.1 Length = 766 Score = 287 bits (735), Expect = 5e-82 Identities = 148/314 (47%), Positives = 200/314 (63%), Gaps = 2/314 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LL V +L + + G V+AVDGI + L GE+LG+VGESG GK+ + ++LRL+ NG Sbjct: 6 LLKVEDLAIHYRTGAGPVQAVDGIHFDLRPGEALGLVGESGCGKTTAAKAMLRLLPPNGE 65 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 + G F G+DL+ L++E +R +R K+I+ I Q M +L+P+ VG Q++E + H + Sbjct: 66 VPRGRIDFDGRDLVALDEESMRKVRWKEIAWISQAAMNALDPVYTVGDQILEAMNAHIKI 125 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 + A A EL VGI P R YP + SGGM+QR +IAMALA PKL+IADEPTT Sbjct: 126 DRKTAWAHAEELFRAVGI--DPGRLSAYPHEMSGGMKQRAVIAMALALDPKLIIADEPTT 183 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDV QAQI+ L +L+ E GM ++FITHD+SV CDR+ MY G I+E PV E+ Sbjct: 184 ALDVVTQAQILARLSKLRRERGMGLLFITHDISVVVQTCDRVAVMYGGHIMETGPVREVF 243 Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEP 303 TP HPYT GL N+ + ++L+ IPG+PP+ PSGC+F RC FA E C RE P Sbjct: 244 GTPFHPYTMGLTNAFPTLEGAQRELISIPGSPPDLLNPPSGCRFAERCPFATERCVRETP 303 Query: 304 PLVNISENHRVACH 317 PL + E + ACH Sbjct: 304 PLHPVGEERQAACH 317 Score = 204 bits (519), Expect = 6e-57 Identities = 119/325 (36%), Positives = 179/325 (55%), Gaps = 18/325 (5%) Query: 4 LLNVNNLKVEFHRVEGI------------VKAVDGISYKLNKGESLGIVGESGSGKSVSV 51 LL V LK F +G V AVDGIS+ L +GE LG+ GESGSGK+ + Sbjct: 362 LLEVEELKKHFPVEQGFLDGLRGRNKDRKVHAVDGISFDLREGEILGLAGESGSGKTTTG 421 Query: 52 LSLLRLINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGI 111 L+RL++ + +GE F G D+ +L EL+ R + +IFQ+P +LNP + Sbjct: 422 EMLVRLLD----VTEGEIRFEGADIAQLTGRELKTFRRR-AQMIFQDPYQTLNPRFTIFD 476 Query: 112 QVMEPIIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALAC 171 V EP+I HRL + E R++ + LER G+ + +P + SGG RQRV IA A+ Sbjct: 477 IVAEPLIIHRLAEGEALRQKVVVALERAGLKPAEVYAERFPHELSGGQRQRVAIARAIVL 536 Query: 172 HPKLLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAG 231 P+ ++ADEP + LDV+I+A ++ L+ + E G+S ++++HDL DR MY G Sbjct: 537 EPRFIVADEPVSMLDVSIRAGVLNLMHRFRNELGISFVYVSHDLPTIRYVADRTAIMYLG 596 Query: 232 KIVEEAPVEEILKTPLHPYTKGLLNSTLEIG-SRGKKLVPIPGNPPNPTKHPSGCKFHPR 290 +IVE P E++++ HPYT+ LL ++ E + K + G P+ + P+GC FH R Sbjct: 597 EIVEVGPTEQVVRERKHPYTQLLLEASPEPDPAVVKPPLESAGEIPSAVEPPNGCHFHTR 656 Query: 291 CSFAMEICQREEPPLVNISENHRVA 315 C AM C E ++ R+A Sbjct: 657 CPRAMAHCGWEGRDVITALSEWRIA 681 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: 630 Number of extensions: 29 Number of successful extensions: 6 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: 766 Length adjustment: 34 Effective length of query: 290 Effective length of database: 732 Effective search space: 212280 Effective search space used: 212280 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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