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 PP_4453 PP_4453 glutathione ABC transporter ATP-binding subunit
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Putida:PP_4453 Length = 610 Score = 265 bits (677), Expect = 2e-75 Identities = 138/269 (51%), Positives = 186/269 (69%) Query: 4 LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63 +L V L V F R G V +S+++ +GE+L IVGESGSGKSVS +S+L L+ N Sbjct: 12 VLEVTGLNVAFRRGGGWSPVVKDLSFRVARGETLAIVGESGSGKSVSAMSILGLLPANTS 71 Query: 64 IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123 V G G++LL L + E+ +IRG I++IFQ PMTSLNP++ +G Q+ EP+ HR + Sbjct: 72 QVTGSIRLQGQELLCLPEPEMADIRGNRIAMIFQEPMTSLNPVMTIGEQIAEPLRLHRGL 131 Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183 +A+E A++L+ERV IP + +R+ +YP QFSGGMRQRVMIAMALAC+P +LIADEPTT Sbjct: 132 DATQAKEEALKLMERVRIPAAQERYDDYPHQFSGGMRQRVMIAMALACNPAVLIADEPTT 191 Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEIL 243 ALDVTIQAQI+EL++EL+ + M+V+FITHD+ V DR + MY G +VE A EI Sbjct: 192 ALDVTIQAQILELIKELQAQEHMAVVFITHDMGVVAQIADRTLVMYRGDLVETASTSEIF 251 Query: 244 KTPLHPYTKGLLNSTLEIGSRGKKLVPIP 272 P PYTK LL++ E+GS + P P Sbjct: 252 SAPQKPYTKALLSAVPELGSMAAEPSPKP 280 Score = 173 bits (439), Expect = 9e-48 Identities = 102/244 (41%), Positives = 145/244 (59%), Gaps = 10/244 (4%) Query: 14 FHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLG 73 F RV G V AV+ +S+ L++GE+L IVGESG GKS + + L++ V E + LG Sbjct: 325 FKRVTGRVHAVENVSFNLSQGETLAIVGESGCGKSTTGRLITGLLDPTHGSVKLEGVELG 384 Query: 74 KDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAI 133 + E R + I ++FQ+P +SLNP V ++EP+ H L + E AI Sbjct: 385 S----ITPME----RARKIQMVFQDPYSSLNPRQTVAQSIIEPLRVHGLYDAKRCEEVAI 436 Query: 134 ELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQI 193 ELL +VG+P L P +FSGG RQRV IA ALA P ++ADE +ALDV+++ QI Sbjct: 437 ELLVKVGLPADAAWRL--PHEFSGGQRQRVCIARALALRPGTIVADEAVSALDVSVKVQI 494 Query: 194 MELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKG 253 + LL EL++E G+ IFI+HD++V R+ MY G+IVE P I P HPYT+ Sbjct: 495 VNLLLELQQELGLGFIFISHDMAVVERVSHRVAVMYMGEIVEIGPRAAIFNDPKHPYTRR 554 Query: 254 LLNS 257 L+++ Sbjct: 555 LIDA 558 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: 471 Number of extensions: 14 Number of successful extensions: 3 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: 610 Length adjustment: 32 Effective length of query: 292 Effective length of database: 578 Effective search space: 168776 Effective search space used: 168776 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: 51 (24.3 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