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_086509748.1 BZY95_RS09770 ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >NCBI__GCF_002151265.1:WP_086509748.1 Length = 618 Score = 249 bits (636), Expect = 1e-70 Identities = 137/274 (50%), Positives = 180/274 (65%), Gaps = 11/274 (4%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLIN-RNG 62 LL+V L V F R E V +S+ L GE+L IVGESGSGKSV+ L+++RL+ +N Sbjct: 6 LLSVEFLSVAFGRNE----VVKNLSFDLQAGETLAIVGESGSGKSVTSLAIMRLVEYQNA 61 Query: 63 RIVDGEAIFLGKD------LLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116 I G F D L +L E+R IRGK+IS+IFQ PMTSLNP+ +G Q+ E Sbjct: 62 LITKGSIRFQRPDTNTYLDLARLTDREMRRIRGKEISMIFQEPMTSLNPVYTIGDQIAEV 121 Query: 117 IIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLL 176 +I H AR+ AI LLE V + ++ YP Q SGGMRQRVMIAMALAC P++L Sbjct: 122 LILHERHDRASARQEAIRLLELVRLADAESLLKRYPHQLSGGMRQRVMIAMALACKPRIL 181 Query: 177 IADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236 +ADEPTTALDVTIQAQI+ ++++L++E GM+VIFITHD+ V D ++ M G+ VEE Sbjct: 182 VADEPTTALDVTIQAQILAIIRDLQKELGMAVIFITHDMGVVAEIADHVVVMREGEKVEE 241 Query: 237 APVEEILKTPLHPYTKGLLNSTLEIGSRGKKLVP 270 APVEEI P PYTK LL++ ++GS + +P Sbjct: 242 APVEEIFAAPREPYTKALLSAVPKLGSMQGQSLP 275 Score = 177 bits (449), Expect = 6e-49 Identities = 104/261 (39%), Positives = 159/261 (60%), Gaps = 17/261 (6%) Query: 4 LLNVNNLKVEFHRVEGI-------VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56 ++ +NNL F +G V AV+ +S ++ GE+L +VGESGSGKS ++ ++ Sbjct: 307 IVRINNLVTRFDIHKGFFGGVSHRVHAVENVSLEIYPGETLALVGESGSGKS-TIGRTIQ 365 Query: 57 LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116 L+ N G+ + G+ + ++++ E +R +++ IFQ+P SL+P VG + EP Sbjct: 366 LLQEN---TSGDIFYSGQLVSQMSRIEKMRLR-QEVQYIFQDPFASLDPRKTVGFSIAEP 421 Query: 117 IIWHRLMKNE-EARERAIELLERVGI-PESPKRFLNYPFQFSGGMRQRVMIAMALACHPK 174 I H L+K + R ELLERVG+ PE +R YP +FSGG RQR+ IA ALA PK Sbjct: 422 IHTHGLLKGRGNVQRRVRELLERVGLRPEHAER---YPHEFSGGQRQRICIARALASRPK 478 Query: 175 LLIADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIV 234 L+IADE +ALDV+IQAQI+ L+ L+ E G++ +FI+HD++V R+ ++ G+IV Sbjct: 479 LIIADEALSALDVSIQAQIIHLMMTLQREEGLAYLFISHDMAVVEKMSHRVAVLHLGQIV 538 Query: 235 EEAPVEEILKTPLHPYTKGLL 255 E P + + P H YT+ LL Sbjct: 539 EMGPRQRVFDAPQHAYTRKLL 559 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: 472 Number of extensions: 15 Number of successful extensions: 4 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: 618 Length adjustment: 32 Effective length of query: 292 Effective length of database: 586 Effective search space: 171112 Effective search space used: 171112 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 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