Align D-gluconate TRAP transporter, large permease component (characterized)
to candidate WP_002720648.1 RSPH17029_RS10760 TRAP transporter large permease
Query= reanno::psRCH2:GFF2081 (425 letters) >NCBI__GCF_000015985.1:WP_002720648.1 Length = 426 Score = 293 bits (750), Expect = 7e-84 Identities = 154/418 (36%), Positives = 250/418 (59%), Gaps = 3/418 (0%) Query: 1 MTVVVFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNLQAGADSFPLLAVP 60 M + + S + + +G P+AF L ++ + + YL V ++ Q L +G + L+A+P Sbjct: 1 MELFILFGSFVFLLLIGTPVAFCLGVSSFLTVLYLGLPPV-VVFQRLNSGVSVYALMAIP 59 Query: 61 FFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAALAT 120 FFI +G+LM G I+RR++A+A A GH RGGLG V + ASV+ +SGSA AD +A+ Sbjct: 60 FFIYSGDLMVRGDIARRLVALAGALVGHLRGGLGQVNVVASVMFGGVSGSAAADASAVGG 119 Query: 121 LLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTG--TSISQLFLAGMVPG 178 L++P M+ RGY + + L G IIA +IPPS +IY + G SI+ LF AG++PG Sbjct: 120 LMVPQMKARGYGVDYAVNLTVVGSIIALMIPPSHNMIIYSIAAGGRISIADLFTAGIIPG 179 Query: 179 LIMGMGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTPT 238 L++ +GL+VA +ARR P + + V L+L +I GG+R G+FT + Sbjct: 180 LLLALGLMVAAYFVARRRGYPTERFPGLRALGAIFVSAVPGLILVALIFGGVRSGIFTAS 239 Query: 239 EAAVVAAVYALAVSTLLYRELNWAGLVEVLTRASRTTASVMFLCAAATVSAYMITLAQLP 298 E+A +A VYAL V+ L+YR L W+ V A RTTA V+ + A +++ ++P Sbjct: 240 ESANIAVVYALLVTILIYRTLTWSEFVHATIGAVRTTAMVLLVIGCAASFGWLLAYLKVP 299 Query: 299 DEIAAMLGPLAQDPKLLMVAIMLLMIAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFG 358 + A + L+ +P ++++ I + ++ +G +D++P I+I P+ P+A G+DPV+FG Sbjct: 300 TALVAFMQGLSDNPLVILLLINVALLVLGTFMDMSPLIVITTPIFLPVAQAFGVDPVHFG 359 Query: 359 VMFVLIGSIGLITPPVGTVLNVVGGIGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSI 416 V+ +L IGL TPPVG VL V +GR+ + T +R + PF+ L ++ L+ +P++ Sbjct: 360 VILILNLGIGLCTPPVGAVLFVGCAVGRISIWTAMRTIWPFYGAALAVLLLVTYIPAL 417 Lambda K H 0.328 0.142 0.413 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: 524 Number of extensions: 18 Number of successful extensions: 3 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: 425 Length of database: 426 Length adjustment: 32 Effective length of query: 393 Effective length of database: 394 Effective search space: 154842 Effective search space used: 154842 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. 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