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 BPHYT_RS12370 BPHYT_RS12370 ABC transporter
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__BFirm:BPHYT_RS12370 Length = 544 Score = 240 bits (613), Expect = 5e-68 Identities = 132/258 (51%), Positives = 177/258 (68%), Gaps = 10/258 (3%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LL +++L V F G AV ++ + +GE + +VGESGSGKSV+ LS+LRL++ Sbjct: 17 LLELDHLHVRF----GDTVAVSDVTLAIQRGERVALVGESGSGKSVTALSILRLLS--DA 70 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 V G F G+DLL + E+R +RG DI++IFQ PMT+LNP+ VG Q+ E I+ H + Sbjct: 71 QVSGSIRFDGEDLLGKTEREMRGMRGSDIAMIFQEPMTALNPLYTVGDQIAETIVVHDGV 130 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 EAR+RA+ LL R GI E KR +YP Q SGG RQR MIAMALAC P+LL+ADEPTT Sbjct: 131 SANEARKRAVALLGRTGIAEPGKRVNSYPHQLSGGQRQRAMIAMALACRPRLLLADEPTT 190 Query: 184 ALDVTIQAQIMELLQELK----EEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPV 239 ALDVTI+AQI++LL EL+ E+ GM+V+ ITHDL++ +F RI M G +VE PV Sbjct: 191 ALDVTIRAQIVDLLLELQRDEAEKRGMAVLLITHDLNLVRHFAQRIAVMEKGVLVESGPV 250 Query: 240 EEILKTPLHPYTKGLLNS 257 E++ ++P HPYT+ LL S Sbjct: 251 EQVFESPQHPYTQRLLAS 268 Score = 173 bits (438), Expect = 1e-47 Identities = 101/243 (41%), Positives = 146/243 (60%), Gaps = 8/243 (3%) Query: 19 GIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLLK 78 G +AV + + +GE+LGIVGESGSGKS ++LL L R V GE F G+ L Sbjct: 308 GRFRAVADANVSVRQGETLGIVGESGSGKSTLAMALLGL----QRTVHGEIEFQGRALGS 363 Query: 79 LNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR-LMKNEEARERAIELLE 137 E +R ++ ++FQ+P +SL+P + V E + HR M + R++ I +L Sbjct: 364 YRGAEQTALRS-NMQVVFQDPFSSLSPRQTIERIVGEGLALHRPAMTPQARRDKVISVLR 422 Query: 138 RVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELL 197 VG+ + + YP +FSGG RQR+ IA AL P++LI DEPT+ALDV+IQ Q+++LL Sbjct: 423 EVGLDRTVLQ--RYPHEFSGGQRQRIAIARALVLEPRILILDEPTSALDVSIQQQVLKLL 480 Query: 198 QELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLLNS 257 L+++Y + +FI+HDL+V R+ M G IVE VEEI TP HPYT+ LL + Sbjct: 481 AGLQQKYNLGFVFISHDLAVIGAMAHRVAVMQNGSIVESGEVEEIFSTPAHPYTRKLLKA 540 Query: 258 TLE 260 L+ Sbjct: 541 ALD 543 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: 415 Number of extensions: 23 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: 544 Length adjustment: 32 Effective length of query: 292 Effective length of database: 512 Effective search space: 149504 Effective search space used: 149504 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