Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate GFF1595 PGA1_c16170 TRAP transporter, 4TM/12TM fusion protein
Query= reanno::psRCH2:GFF84 (674 letters) >FitnessBrowser__Phaeo:GFF1595 Length = 869 Score = 329 bits (844), Expect = 3e-94 Identities = 227/690 (32%), Positives = 347/690 (50%), Gaps = 76/690 (11%) Query: 18 LFYVALLFSIYQIVTAAFHPVSSQVL--------RAGHVGFLLLLVFLCYPARGNGKPFQ 69 L VA+++S++Q+V A+ PVS+ +L R H+ F + L + YPA + + Sbjct: 38 LAIVAVIWSVFQVVLAS--PVSNLLLPGSVVNNSRQIHLAFAIFLAYAAYPALKSSPTDR 95 Query: 70 -PVA-WLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIAL 127 PV W+L L G T Y + F ++ G D + +VL+FE ARR +G A+ Sbjct: 96 IPVQDWILALIGTFTALYGYIFYEKIVNSGGKGDDIDTIFAAIGLVLLFEGARRALGPAM 155 Query: 128 PIICALFLAYGLLG--EYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFI 185 I+ ++F+ Y G E +P + +G LD+ + Q+ +EG++G VS ++FLF+ Sbjct: 156 AIVASVFMLYVFFGSSELVPDVIRWKGASLDRAMEQMWITSEGVFGIALGVSTKFVFLFV 215 Query: 186 LFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTI 245 LFG+ L++AG F A G GH GGPAK +VV SA G I+GS +ANVVTTG FTI Sbjct: 216 LFGALLDKAGAGNYFIKMAFGALGHLRGGPAKAAVVGSAATGLISGSSIANVVTTGTFTI 275 Query: 246 PLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLY 305 PLMKR G+ AG VE SS+ QIMPPVMGA AF+M E + + +VE+ A +PA + Sbjct: 276 PLMKRVGFSSEQAGSVEVASSVNGQIMPPVMGAAAFLMVEYVGISYVEVITHAFLPAAIS 335 Query: 306 FGSVFWMVHLEAKR-----AGLKGLPKDECPSAMAAVKERWYLL---------------- 344 + ++ ++VHLEA + G + + MAA + L Sbjct: 336 YIALVYIVHLEAVKRNMPTLGNRVVSMGRTIGGMAAFFAGFAALCYGIQYPIKAITAAIP 395 Query: 345 ----IPLVVLVWLLFSGRTPMFAGTIGLA------------------------LTAIVIL 376 + L +LV + G + AGT L L I++L Sbjct: 396 GASGLVLSLLVVAAYLGLLWLAAGTDDLVPDDPNAAEVELPVVGEIYKAGLHYLLPIIVL 455 Query: 377 GSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCWFIKGGRDTLVIC 436 ++++ + L AFW L Q + +F + L F+ G D Sbjct: 456 VYFLMIEQKSPGLS-AFWATALLFVILLTQKPLKALFRGQSTLAHS--FLDGVHD----L 508 Query: 437 LHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFLSLLLTMLTC 496 + L++GAR+ + + +A A GVI+G V+LTGV + + + NL L L++ L Sbjct: 509 WNGLIDGARNMIGIALATATAGVIVGTVTLTGVGQVMSELVELMSGGNLILMLIMVGLLS 568 Query: 497 LVLGMGIPTIPNYIITSSIAAPALLDLG------VPLIVSHMFVFYFGIMADLTPPVALA 550 LVLGMG+PT NYI+ SS+ A +++LG VPLI H+FVFYFGIMAD+TPPV LA Sbjct: 569 LVLGMGLPTTANYIVVSSLMAGVVVELGAQSGLVVPLIAVHLFVFYFGIMADVTPPVGLA 628 Query: 551 CFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATLYMLFKAAFAV 610 FAAA ++ ++ A ++ +PF+ ++N L++ W + + A A+ Sbjct: 629 SFAAAAVSGGDAIRTGFVAFFYSLRTVALPFVFIFNTDLLLIDVGWVQGILVAISATIAI 688 Query: 611 GLWGAVFTGYLQRPMALWEKVLAFAAAASM 640 + A Y ++E VL A ++ Sbjct: 689 LAFTAGTMNYFITRNRIYESVLLVLVAFAL 718 Lambda K H 0.330 0.143 0.445 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: 1621 Number of extensions: 93 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 674 Length of database: 869 Length adjustment: 40 Effective length of query: 634 Effective length of database: 829 Effective search space: 525586 Effective search space used: 525586 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 55 (25.8 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