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 GFF996 PGA1_c10130 glutathione import ATP-binding protein GsiA
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Phaeo:GFF996 Length = 606 Score = 258 bits (660), Expect = 2e-73 Identities = 143/314 (45%), Positives = 201/314 (64%), Gaps = 23/314 (7%) Query: 13 LLQTVDLKKYFPQGKRILK-------AVDGISIEIKEGETLGLVGESGCGKSTLGRTILK 65 LL+ +L FP IL+ AV+ +S ++ +G+TL LVGESGCGKS+ GR++L+ Sbjct: 301 LLEVRNLVTRFPVKGGILRRTVANVHAVEDVSFKVFKGQTLSLVGESGCGKSSAGRSLLR 360 Query: 66 LLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHK 125 L+ P G + FEG+DI LN E+ R MQ+IFQDP SLNPQM + + +P+ + Sbjct: 361 LVEPQSGAVEFEGRDILGLNQSELHKARLDMQMIFQDPFASLNPQMQLLDQVAEPMRNYG 420 Query: 126 IGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVS 185 + + E + RV L D V + R F+ +PHE SGGQ+QRI IARALALNPK IV DE VS Sbjct: 421 LASGSELQDRVANLFDRVHLPRSFMRRYPHEMSGGQRQRIAIARALALNPKLIVADEAVS 480 Query: 186 ALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIF 245 ALDVS+QAQ+++L+ E+Q ++G+S+LFI+H++AVVE +SH+V VMYLG+IVE G ++F Sbjct: 481 ALDVSVQAQVLNLMMELQAELGLSFLFISHDMAVVERVSHQVGVMYLGRIVELGPRARVF 540 Query: 246 LNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEK 305 NP H YT+AL+K+VP + +K +PSPI + ++ Sbjct: 541 ENPQHAYTQALMKAVPIADPNQRKSEKDLNFKPIPSPI---------------HDLNYQP 585 Query: 306 EP-ELTEVEKNHFV 318 EP + EVE HFV Sbjct: 586 EPSQYIEVEPGHFV 599 Score = 179 bits (453), Expect = 2e-49 Identities = 102/266 (38%), Positives = 161/266 (60%), Gaps = 13/266 (4%) Query: 11 KPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD 70 +P+ Q L+ F + V +S ++ GET+ +VGESG GKS ++++L+ Sbjct: 4 QPIAQIKGLRVEFQTKDGPVVGVKDVSFDVNPGETVCIVGESGSGKSVSSLSLMRLVEFG 63 Query: 71 GGKI-----FFEGKD-----ITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIED 119 GG I F+ +D + + MK R ++ +IFQ+P+ +LNP TVGR + + Sbjct: 64 GGDITSGQLLFDRRDGSEVDLGKTDQSLMKQIRGNEIGMIFQEPMTALNPVFTVGRQLTE 123 Query: 120 PLIIHKIGTKKERRKRVEELLDMVGIGR--EFINSFPHEFSGGQQQRIGIARALALNPKF 177 L +HK TKKE R ELL V I + +PHE SGG +QR+ IA A+A P+ Sbjct: 124 GLRVHKNMTKKEAETRALELLREVRIPEPERRLKQYPHELSGGMRQRVVIAMAMACEPRL 183 Query: 178 IVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVE 237 ++ DEP +ALDV+IQA+I+ L++ ++++ G + +FI H++AVV ++ +V VM+ G VE Sbjct: 184 LIADEPTTALDVTIQAEILALMDRLKRETGTAVMFITHDMAVVAQMADRVVVMFRGNKVE 243 Query: 238 YGDVDKIFLNPIHPYTRALLKSVPKI 263 G V++IF NP H YT++LL +VPK+ Sbjct: 244 EGTVNEIFENPQHDYTKSLLAAVPKL 269 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: 552 Number of extensions: 20 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: 606 Length adjustment: 32 Effective length of query: 296 Effective length of database: 574 Effective search space: 169904 Effective search space used: 169904 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