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 PfGW456L13_2876 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2876 Length = 525 Score = 211 bits (538), Expect = 2e-59 Identities = 114/260 (43%), Positives = 166/260 (63%), Gaps = 4/260 (1%) Query: 1 MMELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINR 60 M L+ + +L V F V + + GE L +VGESGSGKSV+ S+L+L+ + Sbjct: 1 MTNLIEIRDLSVAFSGQT----VVRNLCLDIRPGECLALVGESGSGKSVTAHSILQLLPQ 56 Query: 61 NGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWH 120 G + G++L+ + +LR +RG I++IFQ PMTSLNP+ + Q+ E ++ H Sbjct: 57 TDTETTGSIRYRGQELVGADAGKLRKLRGNRIAMIFQEPMTSLNPLHSIEKQIGETLLVH 116 Query: 121 RLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADE 180 + + + A+ R +ELL VGI + +R YP Q SGG RQRVMIAMALAC P+LLIADE Sbjct: 117 KGLAGKAAQARILELLHLVGIQKPEERLKAYPHQLSGGQRQRVMIAMALACEPELLIADE 176 Query: 181 PTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVE 240 PTTALDVT+Q +I+ LL+ L++ GMS++ I+HDL++ + R+ M AG+IVE+AP E Sbjct: 177 PTTALDVTVQRKILLLLKSLQQRLGMSLLLISHDLNLVRSIAQRVCVMKAGEIVEQAPCE 236 Query: 241 EILKTPLHPYTKGLLNSTLE 260 + P HPY+ LL++ E Sbjct: 237 TLFTEPRHPYSCILLHAEPE 256 Score = 183 bits (464), Expect = 9e-51 Identities = 108/263 (41%), Positives = 161/263 (61%), Gaps = 16/263 (6%) Query: 4 LLNVNNLKVEFHRVEGI------VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRL 57 +L V+NL+V F G+ ++AVDGIS + +G++LGIVGESGSGKS ++LRL Sbjct: 268 VLEVDNLQVRFPVGGGLFQRKTWLRAVDGISLNIQRGKTLGIVGESGSGKSTLGQAILRL 327 Query: 58 INRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPI 117 ++ G I F G+ L L +++LR R K + ++FQ+P SL+P + V + E + Sbjct: 328 LDSEGGIR-----FQGQALDGLTQKQLRPWR-KKMQVVFQDPFGSLSPRMSVAQIISEGL 381 Query: 118 IWHRLMKNEEARERAIELLERVGI-PESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLL 176 H + EE I L VG+ P+S R YP +FSGG RQR+ IA AL P L+ Sbjct: 382 EVHSQLSTEECNAEVIRALNEVGLDPQSRHR---YPHEFSGGQRQRIAIARALVLKPALI 438 Query: 177 IADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236 + DEPT+ALD T+Q Q++ LL++L+E+YG++ +FI+HDL+V +I + GK+VE Sbjct: 439 LLDEPTSALDRTVQKQVVALLRQLQEKYGLTYLFISHDLAVVRALAHDMIVIKDGKVVER 498 Query: 237 APVEEILKTPLHPYTKGLLNSTL 259 E+ +P HPYTK LL + + Sbjct: 499 GASHEVFDSPQHPYTKELLAAAM 521 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: 404 Number of extensions: 14 Number of successful extensions: 4 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: 525 Length adjustment: 31 Effective length of query: 293 Effective length of database: 494 Effective search space: 144742 Effective search space used: 144742 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