Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate 3607230 Dshi_0646 TRAP transporter, 4TM/12TM fusion protein (RefSeq)
Query= reanno::psRCH2:GFF84 (674 letters) >FitnessBrowser__Dino:3607230 Length = 700 Score = 245 bits (626), Expect = 4e-69 Identities = 168/540 (31%), Positives = 269/540 (49%), Gaps = 58/540 (10%) Query: 15 PRALFYVALLFSIYQIVTAAFHPVSSQVLR-AGHVGFLLLLVFLCYPARGNGKPFQPVAW 73 P L VA + AF PV S++ R A H L L YP G+ V Sbjct: 18 PGTLIAVASFLIAVGHIYVAFDPVLSELQRNAFHFAGFAALAALFYPI-ARGRLALGVDL 76 Query: 74 LLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPIICAL 133 +LGL A Y Y E + R TAD + + +++ E RR+ G +P + + Sbjct: 77 VLGLVVAAAAVYLSYAEDGIYDRGVKFNTADWIAAIIVVLGAIELTRRLTGWIIPALIVI 136 Query: 134 FLAYGLL-GEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGSFLE 192 L+Y + G+++ G G L+ ++ + +G + ++G+ +S+TY+FLFI+FG+FL Sbjct: 137 ALSYVVWWGKFVGGVFNFPGLKLESVLFRSVYGDDAMFGSIASISSTYVFLFIIFGAFLL 196 Query: 193 QAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMKRFG 252 ++G + + A + G +GGP V+V++S L GTI+GS VAN +TG TIPLMKR G Sbjct: 197 RSGAGEFVINLARAVAGRMVGGPGIVAVIASGLTGTISGSAVANTASTGVITIPLMKRAG 256 Query: 253 YRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSVFWM 312 ++P FAGGVEA +S G Q+MPP+MGA AF+MA +P+ I A +PALLYF SV + Sbjct: 257 FQPKFAGGVEAAASTGGQLMPPIMGAGAFVMASFTAIPYETIVAVAALPALLYFLSVAFF 316 Query: 313 VHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRTPMFAGTIGLALTA 372 V +EA+R L + + A ++ ++P+ +L+ +L SG TP +A G+ Sbjct: 317 VRIEARRQNLPPMADEGQTLRRAFLEGGASFVLPIGLLIGMLVSGFTPTYAAVFGI---- 372 Query: 373 IVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGVIFGVIAALVAVCWFIKGGRDT 432 I ++ S+ + + ++G +F + Sbjct: 373 IAVVASSWLTRT---------------------RMGPRAVF-----------------EA 394 Query: 433 LVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFLSLLLT 492 LV+ ++ A VG+ ++ V++ GV +TF+ I A N+ ++++L Sbjct: 395 LVMGTKGMILTAVLLCSVGL-------VVNVIATAGVGNTFSLMIAAWSGGNILVAIVLI 447 Query: 493 MLTCLVLGMGIPTIPNYIITSSIAAPALLDLGVPLIVSHMFVFYFGIMADLTPPVALACF 552 L LVLGMG+P YI+ ++++APAL + +V I A PP A A F Sbjct: 448 ALASLVLGMGLPVTAAYIVLATLSAPALAGMIADQVVIAQ------IAAGTLPPTAQAIF 501 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: 1391 Number of extensions: 88 Number of successful extensions: 6 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: 674 Length of database: 700 Length adjustment: 39 Effective length of query: 635 Effective length of database: 661 Effective search space: 419735 Effective search space used: 419735 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: 54 (25.4 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