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 H281DRAFT_01032 H281DRAFT_01032 peptide/nickel transport system ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Burk376:H281DRAFT_01032 Length = 340 Score = 271 bits (692), Expect = 2e-77 Identities = 149/316 (47%), Positives = 196/316 (62%), Gaps = 1/316 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLI-NRNG 62 +L+V + F + VD +S+ ++ GE+L +VGESG GKSV+ L+L+ L+ + Sbjct: 9 VLDVQGFSLSFSNLPDAPNVVDRVSFLVHAGETLCVVGESGCGKSVTSLALMGLLASPPA 68 Query: 63 RIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122 R V G A F G DL L++ EL +IRG +S+IFQ PMTSLNP VG Q+ E I HR Sbjct: 69 RRVAGTAHFEGVDLFGLSERELADIRGNRMSMIFQEPMTSLNPAYTVGEQIGESIRRHRG 128 Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 + ARE A+++L V IP R + Q SGGMRQRVMIAMALA P+LLIADEPT Sbjct: 129 VSRAAAREEALKMLRLVHIPAPETRLDAFAHQLSGGMRQRVMIAMALANSPRLLIADEPT 188 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 TALDVTIQAQ++ L++ L++E G +++ ITHDL V D + MYAGKIVE V ++ Sbjct: 189 TALDVTIQAQVLALVRNLQKETGTAMLLITHDLGVVAEVADHVAVMYAGKIVEYGTVSDL 248 Query: 243 LKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREE 302 P HPYT GL+ + +G R L I G+ P P + P GC+F PRC FA + C Sbjct: 249 FDDPQHPYTIGLMGAIPSVGKREGSLATIRGSVPTPEQMPRGCRFAPRCPFAEQRCIDAA 308 Query: 303 PPLVNISENHRVACHL 318 PP + HRVAC L Sbjct: 309 PPERTLEGEHRVACWL 324 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: 264 Number of extensions: 6 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 324 Length of database: 340 Length adjustment: 28 Effective length of query: 296 Effective length of database: 312 Effective search space: 92352 Effective search space used: 92352 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: 49 (23.5 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