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 Ac3H11_694 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_694 Length = 341 Score = 224 bits (571), Expect = 2e-63 Identities = 126/315 (40%), Positives = 191/315 (60%), Gaps = 6/315 (1%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 LL + +L+ F V+AVD +S+ +++GE+LG+VGESGSGKS L RL++ Sbjct: 20 LLEIAHLRKHFGSGPHPVRAVDDVSFTIHRGETLGLVGESGSGKSTIGRLLTRLVDPTSG 79 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 + +DL +L++ + R +R + I IIFQ+P SLNP +R+ + E + H L Sbjct: 80 QMRYHGGAAPQDLAQLSQSQYRPLRSQ-IQIIFQDPYASLNPRMRIRDVLAEALDTHGLA 138 Query: 124 KNEEARERAIELLERVGI-PESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 K R +LLE+VG+ PE +RF P +FSGG RQR+ IA ALA P+ ++ADEP Sbjct: 139 KGAARLPRIHQLLEQVGLRPEHAERF---PHEFSGGQRQRIGIARALAVEPQFIVADEPL 195 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 +ALDV+IQAQ++ LL ELKE+ G++++FI+HDL V CDR++ +Y G+++E AP E + Sbjct: 196 SALDVSIQAQVVNLLGELKEQLGLTLLFISHDLDVVEYLCDRVVVLYLGRVMEIAPTEAL 255 Query: 243 LKTPLHPYTKGLLNST-LEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301 P HPYT+ LL + + ++ + + + G+ P+P PSGC F RC A C Sbjct: 256 YAQPQHPYTQALLAAAPIPDPAQRRSIALLQGDLPSPANPPSGCVFRTRCPQAEARCASA 315 Query: 302 EPPLVNISENHRVAC 316 + L ++ H AC Sbjct: 316 DMQLREVAPGHLHAC 330 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: 273 Number of extensions: 13 Number of successful extensions: 4 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: 341 Length adjustment: 28 Effective length of query: 296 Effective length of database: 313 Effective search space: 92648 Effective search space used: 92648 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