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 GFF3629 PGA1_262p00330 oligopeptide ABC transporter, ATP binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Phaeo:GFF3629 Length = 332 Score = 297 bits (761), Expect = 2e-85 Identities = 150/313 (47%), Positives = 205/313 (65%), Gaps = 1/313 (0%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 +L V NL F R ++ AV +S+ + +GE LG+VGESGSGKSV++ S+L L R+G Sbjct: 9 VLEVRNLCTTFKRGGVLLPAVRDVSFDVRQGEVLGLVGESGSGKSVTLRSILGLTRRHGE 68 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 + GE + G+D+ +L+ +LR +RG ++++IFQ PMTSLNP++ VG+Q+ E + H + Sbjct: 69 VT-GEVRWQGRDISRLSDRQLRQVRGGEVAMIFQEPMTSLNPLLTVGLQLTETLKAHTDL 127 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 R RAIE+L+ VGIP + R +YP QFSGGMRQRVMIA+ALA PKLL+ADEPTT Sbjct: 128 SRAARRNRAIEMLDHVGIPAAASRLQDYPHQFSGGMRQRVMIAIALAAEPKLLLADEPTT 187 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDVTIQAQI++L+ L +E M VI +THDL V C+ + MYAG+IVE+ V ++L Sbjct: 188 ALDVTIQAQILDLILRLSQEMNMGVILVTHDLGVVAQTCENVAVMYAGRIVEQGAVRQVL 247 Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEP 303 + P HPYT GL+ S + + L +PG PP+ P GC + PRC E C + P Sbjct: 248 RAPRHPYTAGLMRSVPQDIAPRTPLYSVPGTPPSLEMLPRGCAYAPRCEVRTEACLSKRP 307 Query: 304 PLVNISENHRVAC 316 L IS R AC Sbjct: 308 ALETISAGRRAAC 320 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: 253 Number of extensions: 9 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: 332 Length adjustment: 28 Effective length of query: 296 Effective length of database: 304 Effective search space: 89984 Effective search space used: 89984 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