Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Ac3H11_2052 Putative glutathione transporter, ATP-binding component
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2052 Length = 345 Score = 273 bits (699), Expect = 3e-78 Identities = 147/334 (44%), Positives = 216/334 (64%), Gaps = 17/334 (5%) Query: 8 IKMKPLLQTVDLKKYFP------------QGKRILKAVDGISIEIKEGETLGLVGESGCG 55 +K K L+Q DL K F + + +L AVDG+S EI++G+TL LVGESGCG Sbjct: 14 VKSKALVQAHDLAKTFDVSAPWLNRVIERKPRTLLHAVDGVSFEIEKGKTLALVGESGCG 73 Query: 56 KSTLGRTILKLLRPDGGKIFFEGKDI-TNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVG 114 KST+ R ++ L P G + F+ +D K+ + R+++Q+IFQDP SLNP+ V Sbjct: 74 KSTVARLLVGLYEPTRGGLTFDNQDAHAAFKGKDAQAMRRRIQMIFQDPYASLNPRWLVE 133 Query: 115 RIIEDPLIIHKIGTKK-ERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALAL 173 II +PL H + T K E + RV ELL VG+ + +PH+FSGGQ+QRI IARALA Sbjct: 134 DIIGEPLREHGLITDKAELKARVGELLKSVGLSPLDMVKYPHQFSGGQRQRISIARALAT 193 Query: 174 NPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLG 233 P+F+VCDEP SALDVS+QAQ++++++++Q++ ++YLFI+HNLAVV H+S +V VMYLG Sbjct: 194 EPEFLVCDEPTSALDVSVQAQVLNIMKDLQRERQLTYLFISHNLAVVRHVSDQVGVMYLG 253 Query: 234 KIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQT 293 ++VE D ++F +P HPYTR LL ++PK+ G+ + ++GE+P+P++ P GC F Sbjct: 254 RLVELADKHQLFNSPRHPYTRMLLDAIPKMHDTGKART--PVQGEVPNPLNPPPGCAFNP 311 Query: 294 RCTEKKAICFEKEPELTEVEKNHFVSCHLVRSYR 327 RC C + P+L + ++CH V R Sbjct: 312 RCPHVNDRCRTERPKLLSIGGIR-IACHAVEEGR 344 Lambda K H 0.321 0.142 0.417 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: 357 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: 328 Length of database: 345 Length adjustment: 28 Effective length of query: 300 Effective length of database: 317 Effective search space: 95100 Effective search space used: 95100 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