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 BPHYT_RS15540 BPHYT_RS15540 glutathione ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__BFirm:BPHYT_RS15540 Length = 640 Score = 266 bits (681), Expect = 8e-76 Identities = 136/279 (48%), Positives = 192/279 (68%), Gaps = 7/279 (2%) Query: 12 PLLQTVDLKKYFPQGKRI-------LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64 P+L+ DL FP + + AV+ +S +++ GETL LVGESGCGKST GR++L Sbjct: 332 PILRVRDLVTRFPVKSGLFGRLTGRVHAVEKVSFDLRPGETLALVGESGCGKSTTGRSLL 391 Query: 65 KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 +L+ G I F GK+I++L ++ R+ +Q IFQDP SLNP++TVG I +PL++H Sbjct: 392 RLVESQSGSIEFNGKEISSLTGPALQALRRDIQFIFQDPFASLNPRLTVGFSIMEPLLVH 451 Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 + E + RV+ LLD VG+ E +PHEFSGGQ+QRI IARALALNPK ++ DE V Sbjct: 452 GVAQGAEAQARVQWLLDKVGLPSEAARRYPHEFSGGQRQRIAIARALALNPKVVIADESV 511 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALDVS+QAQI++L+ ++Q+++G++YLFI+H++AVVE +SH+VAVMYLG+IVE G + Sbjct: 512 SALDVSVQAQIVNLMLDLQRELGVAYLFISHDMAVVERVSHRVAVMYLGQIVEIGPRRAV 571 Query: 245 FLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPI 283 F P HPYTR L+ +VP + + E+PSPI Sbjct: 572 FEAPQHPYTRKLMGAVPVADPARRHAKRMLAADEIPSPI 610 Score = 177 bits (450), Expect = 5e-49 Identities = 102/275 (37%), Positives = 156/275 (56%), Gaps = 22/275 (8%) Query: 11 KPLLQTV---------DLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGR 61 +PL++T+ DL F G AV +S+ ++ GETL +VGESG GKS Sbjct: 9 RPLIETLPPQRVLAVDDLSVAFRSGDTTFNAVRNLSLTVERGETLAIVGESGSGKSVTSL 68 Query: 62 TILKLL-----RPDGGKIFFEGKD-----ITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQ 110 +++L+ R GG I F +D + + M+ R + +IFQ+P+ SLNP Sbjct: 69 ALMRLIEHGGGRLAGGSIAFRRRDGSVLDLAKASSGTMRSIRGADIAMIFQEPMTSLNPV 128 Query: 111 MTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGI--GREFINSFPHEFSGGQQQRIGIA 168 TVG I + + +H+ ++ LL++V I R FPH+ SGG +QR+ IA Sbjct: 129 FTVGDQISEAIALHQGKSRSAAHAETLRLLELVRIPEARRVAARFPHQLSGGMRQRVMIA 188 Query: 169 RALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVA 228 AL+ P ++ DEP +ALDV+IQAQI+ L+ +Q +M + +FI H++ VV ++ +V Sbjct: 189 MALSCKPALLIADEPTTALDVTIQAQILQLIRGLQDEMNMGVIFITHDMGVVAEVADRVL 248 Query: 229 VMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKI 263 VMY G+ VE G D +F P HPYT+ALL +VP++ Sbjct: 249 VMYRGEKVEEGASDALFAAPSHPYTKALLAAVPRL 283 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: 553 Number of extensions: 25 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: 328 Length of database: 640 Length adjustment: 33 Effective length of query: 295 Effective length of database: 607 Effective search space: 179065 Effective search space used: 179065 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