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 Pf1N1B4_5104 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5104 Length = 324 Score = 274 bits (701), Expect = 2e-78 Identities = 144/315 (45%), Positives = 201/315 (63%), Gaps = 1/315 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 +L V L V + E V VD +S+ L +GE LG+VGESGSGK+++ L+RL+ Sbjct: 1 VLKVEELSVIVRKGEHEVTLVDRLSFDLAEGEVLGLVGESGSGKTLACRGLMRLLPSPNL 60 Query: 64 IVDGEAIFL-GKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122 V+G A+ L G++LL L++ +R +RG+ + +IFQNP + L+P++R+G Q+ E I H+ Sbjct: 61 RVEGTAVQLAGENLLHLDEAGMRRMRGRQLGMIFQNPSSHLDPLMRIGEQIGEGIRLHQG 120 Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182 EAR +AI++L +VGIP+ +R +YP +FSGGMRQR MIA+AL C+P +LIADEPT Sbjct: 121 ASRREARAQAIDVLRQVGIPDPQRRVDSYPHEFSGGMRQRAMIAVALGCNPNVLIADEPT 180 Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242 TALDVT+QAQI+ LL +L+++ G+S+I ITHDL V CD I MYAG++ E E+ Sbjct: 181 TALDVTVQAQILRLLLDLRDQRGLSIIMITHDLGVVAQTCDSIAVMYAGRLCEHGNKHEV 240 Query: 243 LKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREE 302 L P HPYT GL++ L I G PP P GC+F+PRC C Sbjct: 241 LAHPRHPYTAGLIDCQPATSHGHALLNTIAGQPPLLDALPQGCRFNPRCQQIGNRCTTLM 300 Query: 303 PPLVNISENHRVACH 317 P L +S HR+ACH Sbjct: 301 PGLQPVSHGHRIACH 315 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: 307 Number of extensions: 14 Number of successful extensions: 2 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: 324 Length adjustment: 28 Effective length of query: 296 Effective length of database: 296 Effective search space: 87616 Effective search space used: 87616 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: 48 (23.1 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