Align TRAP-type large permease component (characterized, see rationale)
to candidate GFF2912 PS417_14900 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__WCS417:GFF2912 Length = 426 Score = 314 bits (805), Expect = 3e-90 Identities = 158/424 (37%), Positives = 260/424 (61%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 M ++ + L M +GVP+A SL G V + + +A + +D +T LAIP Sbjct: 1 MAVLCLFLLLFVFMFLGVPIAISLGLSGAVSILMFSQDSVSSLAIKLFETSDAYTFLAIP 60 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FF+L+G M GG+++R+IDFA ACVGHIRGGL I A++A ++ A++SGS+ A AA+ + Sbjct: 61 FFLLSGAFMTTGGVAQRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLI 180 I + M ++GY AG+I G + +IPPS+ +V+ A S+ +LFMAG++PGL+ Sbjct: 121 IAVAGMVRSGYPKAFGAGIICNAGTLGILIPPSIVMVVYSAATETSVGKLFMAGVIPGLL 180 Query: 181 MGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEA 240 +G+ L+ +V R + PR +E + + RA W L + VIILGGI +G+ TPTEA Sbjct: 181 LGLMLMIAIYIVARIKKLPAQPRATFREWLTSARRAFWGLLLLVIILGGIYSGMFTPTEA 240 Query: 241 AVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSE 300 A VAAVY+ FV + IY++++ RD P V+L++ + ++MF++ A++ + ++T IP E Sbjct: 241 AAVAAVYSAFVALFIYKDMQLRDCPKVLLESGRLAIMLMFIIANAMLFAHVLTTEQIPQE 300 Query: 301 ITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVL 360 IT ++ P + ++ +V+L+ G+ ++ + +LIL P+ PI + GIDP++ G++ Sbjct: 301 ITAWVLSEGLTPIGFLIMVNVVLLIAGSFMEPSAIVLILAPIFFPIAMKLGIDPIHLGIV 360 Query: 361 FIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVIVP 420 ++N IGL+ PPVG+ L V S V + LG+ I P+L+ ++ L ++ P I + Sbjct: 361 MVVNMEIGLVHPPVGLNLFVTSAVTGLTLGQTIRAALPWLMILLVFLIMVTYLPFISLAL 420 Query: 421 ARWL 424 WL Sbjct: 421 PHWL 424 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: 448 Number of extensions: 15 Number of successful extensions: 2 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 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 51 (24.3 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