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 HSERO_RS09190 HSERO_RS09190 ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__HerbieS:HSERO_RS09190 Length = 617 Score = 243 bits (621), Expect = 7e-69 Identities = 132/266 (49%), Positives = 178/266 (66%), Gaps = 6/266 (2%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNG- 62 +L+VN+L V F E V AV +S+ +++GE+L IVGESGSGKSVS L+++RLI G Sbjct: 7 VLDVNHLSVRFSTSERTVDAVRDLSFHVDQGETLAIVGESGSGKSVSSLAIMRLIEHGGG 66 Query: 63 RIVDGEAIFLGK-----DLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPI 117 +I G FL + DL + + +R+IRG +I++IFQ PMTSLNP+ VG Q+ E I Sbjct: 67 KIASGSMQFLRRSGQRLDLAQADNATMRSIRGAEIAMIFQEPMTSLNPVFTVGEQIAESI 126 Query: 118 IWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLI 177 H+ + A+ A+ +LE V IPE+ + +P Q SGGMRQRVMIAMAL+C P LLI Sbjct: 127 RLHQGLGRAAAQAEALRMLEMVRIPEAKRVLGRHPHQLSGGMRQRVMIAMALSCKPSLLI 186 Query: 178 ADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEA 237 ADEPTTALDVTIQAQI++L++ L++E M VIFITHD+ V DR++ M G+ VEE Sbjct: 187 ADEPTTALDVTIQAQILQLIRSLQQEMQMGVIFITHDMGVVAEVADRVVVMCRGEKVEEN 246 Query: 238 PVEEILKTPLHPYTKGLLNSTLEIGS 263 V + P HPYT+ LL + +GS Sbjct: 247 AVNPLFAAPAHPYTQSLLAAVPRLGS 272 Score = 207 bits (527), Expect = 5e-58 Identities = 130/312 (41%), Positives = 183/312 (58%), Gaps = 29/312 (9%) Query: 14 FHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLG 73 F RV V AV+ +S+ L GE+L IVGESG GKS + SLLRL++ I G+ F G Sbjct: 329 FGRVRQRVHAVEKVSFDLYAGETLAIVGESGCGKSTTGRSLLRLVD----IAGGKVEFGG 384 Query: 74 KDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAI 133 +DL +L + ELR +R +DI IFQ+P SL+P + VG +MEP++ H + E A+ER Sbjct: 385 RDLAQLPRSELRQLR-RDIQFIFQDPFASLDPRMTVGYSIMEPMLVHGM--KEGAQERVD 441 Query: 134 ELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQI 193 LL RVG+ +P+ YP +FSGG RQR+ IA ALA +PK++IADE +ALDV+IQAQI Sbjct: 442 ALLTRVGL--TPEHGQRYPHEFSGGQRQRICIARALALNPKIVIADESVSALDVSIQAQI 499 Query: 194 MELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKG 253 + L+ +L+ E G+S IFI+HD++V R+ MY G+IVE P I + P HPYT+ Sbjct: 500 VNLMLDLQAELGISFIFISHDMAVVERISHRVAVMYLGQIVEIGPRRAIFENPQHPYTRK 559 Query: 254 LLNST----LEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPPLVNIS 309 L+ + + GKKL + P+P + + + PL ++ Sbjct: 560 LMAAVPVADPTLRQPGKKL--LTDEIPSPIRRVGD--------------EPKVEPLQEVA 603 Query: 310 ENHRVACHLIKG 321 H VA H I G Sbjct: 604 PGHFVAQHRIAG 615 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: 487 Number of extensions: 24 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: 617 Length adjustment: 32 Effective length of query: 292 Effective length of database: 585 Effective search space: 170820 Effective search space used: 170820 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: 51 (24.3 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