Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__psRCH2:GFF3103 Length = 394 Score = 242 bits (617), Expect = 1e-68 Identities = 149/379 (39%), Positives = 215/379 (56%), Gaps = 16/379 (4%) Query: 8 QGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGE 67 + PF D R+ WV+Q+L +L V +L N NL+ RG++ F +L+ +AGF I + Sbjct: 12 RSPF-TDPRIRAWVFQVLAVLAVVAFGWYLFHNTQTNLAHRGITSGFGFLNNAAGFGISQ 70 Query: 68 SAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVA 127 I Y +D+Y R VGL+N+L V IG+ L TV+G + GV S NWL+RQL+ Y+ Sbjct: 71 HLIDYSESDTYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIE 130 Query: 128 VVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPG-----WLVV 182 + RN P LL + YF ++ LP + ++++ +G+ +P P WL + Sbjct: 131 IFRNIPPLLLIFFVYFAVISPLPGPRNSLSLWDVVFVNNRGVQMPAPSAGDGFWAFWLAL 190 Query: 183 ILA-IALVLFVSWLAQRQRS-----PRDWR--WLYGAIAVVTVLMLLTQLSWP-QQLQPG 233 ++A +A+V+ W R+ + P W L+ AI + + +W +LQ Sbjct: 191 LVALVAVVVLNRWARARRHATGRMFPVFWTSPGLFLAIPWLMTFIAGAPFTWEVPELQRF 250 Query: 234 QIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQI 293 IRGG + E ++++ L YT AFI E +R GI SV GQ EAAA+LGL Q L + Sbjct: 251 NIRGGWVVIPELVSIVVALSVYTAAFIGETVRSGIQSVSHGQTEAAASLGLRPGQVLRLV 310 Query: 294 VVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEVFLILMLT 352 +VPQALRVIVP L SQY+ AKNSSLA A+GYPD+ + A T LNQTG+ +E I M Sbjct: 311 IVPQALRVIVPPLTSQYLNLAKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETMAITMSV 370 Query: 353 YLAINAVISAGMNGLQQRL 371 YLAI+ IS MN +R+ Sbjct: 371 YLAISISISLLMNWYNKRI 389 Lambda K H 0.326 0.140 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: 438 Number of extensions: 25 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: 377 Length of database: 394 Length adjustment: 30 Effective length of query: 347 Effective length of database: 364 Effective search space: 126308 Effective search space used: 126308 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: 50 (23.9 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