Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_068175617.1 HTA01S_RS22750 DUF3394 domain-containing protein
Query= reanno::psRCH2:GFF84 (674 letters) >NCBI__GCF_001592305.1:WP_068175617.1 Length = 865 Score = 374 bits (961), Expect = e-108 Identities = 238/652 (36%), Positives = 351/652 (53%), Gaps = 77/652 (11%) Query: 10 SPSEW-PRALFYVALLFSIYQIVTAAFHPVSSQVL-------RAGHVGFLLLLVFLCYPA 61 +P W R L Y+AL +S++Q+ A+ P S VL RA H+ F + L ++ YPA Sbjct: 24 APGPWVSRLLLYLALAWSLFQLWIASPLPFSLGVLVFNDTETRAIHLAFAVFLSYMAYPA 83 Query: 62 -RGNGKPFQP-VAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAA 119 R + + P + W L G Y + F ++L R G T D++ + L+ EA Sbjct: 84 FRRSPRDHVPLIDWALAFVGAFCASYLFLFYSELATRPGQPTQMDVITAAVGMALLLEAT 143 Query: 120 RRVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSAT 179 RRV+G+ + I+ +FL Y G Y+P +AHRG+ L++ ++ TEG++G VS++ Sbjct: 144 RRVLGLPMVIVALVFLIYTFGGPYMPDMIAHRGFSLNRAMSHQWLTTEGVFGVALGVSSS 203 Query: 180 YIFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVT 239 +IFLF+LFG+ L++AG F A L GH GGPAK +V+SSA G I+GS +ANVVT Sbjct: 204 FIFLFVLFGALLDKAGAGNYFIKSAFALLGHMRGGPAKAAVLSSAATGIISGSSIANVVT 263 Query: 240 TGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAAL 299 TG FTIPLMKR GYR AG VE +SS+ QIMPPVMGA AF+M E + +P++E+ K A Sbjct: 264 TGTFTIPLMKRVGYRADQAGAVEVSSSVNGQIMPPVMGAAAFLMVEYVGIPYIEVMKHAF 323 Query: 300 IPALLYFGSVFWMVHLEAKRAGLKGLPKDECPS--------------------------- 332 +PA++ + ++ ++VHLEA +A + GLP+ + Sbjct: 324 LPAIISYIALLYIVHLEALKANMVGLPRRNPGTHGSRLLAFALTVAGFLALSGAVYWGIG 383 Query: 333 ---AMAAVKERWY----LLIPLVVLVWLLFSGRTPMF---------------AGTI--GL 368 ++A W LL V L+W F R P+ A T+ GL Sbjct: 384 WIKSVAGDAAIWIVGAGLLAAYVGLLW--FGARQPVLELDDPNAPVFELPETAPTVKSGL 441 Query: 369 -ALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCWFIK 427 L A+V+L ++++ + L AFW L ++ Q I F L + Sbjct: 442 HYLLAVVVLIWCLMVEQMSPGLS-AFWATLFMIFVMLTQKPISAAFRGHGGLA------Q 494 Query: 428 GGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFL 487 R + L GAR+ + +G+A A G+I+G VSLTGV + + NL L Sbjct: 495 ATRQGFADLIDGLATGARNMIGIGVATAAAGIIVGTVSLTGVGLVMTELVELLSGGNLML 554 Query: 488 SLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLG------VPLIVSHMFVFYFGIMA 541 L+L L L+LGMG+PT NYI+ S++ AP +++LG VPLI H+FVFYFG+MA Sbjct: 555 MLVLVALISLILGMGLPTTANYIVVSTLMAPVVVELGAQSGLIVPLIAVHLFVFYFGLMA 614 Query: 542 DLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQG 593 D+TPPV LA FAAA IA+ +K + A ++ I+PF+ ++N L++ G Sbjct: 615 DVTPPVGLASFAAAAIARADPIKTGITAFAYSMRTAILPFLFIFNTQLLLMG 666 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: 1721 Number of extensions: 96 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: 865 Length adjustment: 40 Effective length of query: 634 Effective length of database: 825 Effective search space: 523050 Effective search space used: 523050 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 24 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