Align TRAP-type large permease component (characterized, see rationale)
to candidate RR42_RS10605 RR42_RS10605 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS10605 Length = 615 Score = 252 bits (644), Expect = 2e-71 Identities = 143/411 (34%), Positives = 234/411 (56%), Gaps = 7/411 (1%) Query: 8 VSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIPFFILAGE 67 + +GA+ +GVP+ F L F ++ + +Q ++AG D F LLAIPFF+LAG Sbjct: 196 IGFIGALVLGVPIGFVLAFAALLYFLADPSLPMLVYSQQVMAGTDHFVLLAIPFFVLAGL 255 Query: 68 LMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIPMMA 127 LM A G+S R+I+ + G +RGGLG++ I+A + +SGS AD AA+ I++P + Sbjct: 256 LMEANGMSSRLIELLLRVFGRVRGGLGLITIIATAFFSGVSGSKLADVAAVGGIVMPAVR 315 Query: 128 KAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGIALVA 187 + + +AGL+A V+A IPP + I+ G AN+SI LFMAG+VP +M ++L Sbjct: 316 RTRQDPGEAAGLLACSAVMAETIPPCINLILMGFVANISIAGLFMAGLVPAAVMALSLAV 375 Query: 188 TWLLVVRK--DDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVVAA 245 ++V RK D RTP+ +G AL AL M +I G+ +G+ T TE + A Sbjct: 376 LAVIVGRKINPDEAFEHRTPLWPLLGG---ALVALIMVGMIGKGVTSGIATSTEVSAFAV 432 Query: 246 VYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFI 305 VYAL VG + +REL R + + +++A I+F+V AA S+ +T IP ++G + Sbjct: 433 VYALVVGGLAFRELNLRSVARLFVRSASMAGGILFIVAAASSVSFALTIEQIPQLMSGTM 492 Query: 306 SPLIDRPTLLMFVIM--LVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIM 363 + + +MF+++ L+++V G L+ P ++I P+L PI +Q G++P++FG + ++ Sbjct: 493 TAFAAQYGSVMFIMLSALLMMVFGAVLEGAPALIIFGPLLTPIAQQLGVNPLHFGTVMVI 552 Query: 364 NTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFP 414 +GL PPVG+ L + + V + +L ++ L LL+L P Sbjct: 553 AMGLGLFAPPVGLGLFATCAITGTQVKDVARPMLKYLAVLLVALVLLILVP 603 Lambda K H 0.331 0.145 0.430 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: 659 Number of extensions: 34 Number of successful extensions: 4 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: 615 Length adjustment: 35 Effective length of query: 390 Effective length of database: 580 Effective search space: 226200 Effective search space used: 226200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 52 (24.6 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