Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate GFF195 PGA1_c01990 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__Phaeo:GFF195 Length = 410 Score = 207 bits (527), Expect = 4e-58 Identities = 138/380 (36%), Positives = 203/380 (53%), Gaps = 28/380 (7%) Query: 14 DERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYR 73 D R +Q + LV+ L +L +NL+ NL GL++S+ +L +G++I + I Y Sbjct: 20 DTRYRSLTFQAIAALVLALAIWYLGNNLIQNLRAAGLNISYGFLGDPSGYDINQRLIEYD 79 Query: 74 TADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTP 133 + S+ARA VVG++N+L V + I T+ G +AGV S NWL+ +L YV + RN P Sbjct: 80 SQSSHARAAVVGVLNTLLVAVLACITATIFGVVAGVLRLSNNWLVSKLMAVYVEIFRNIP 139 Query: 134 LLLQLIVWYFPILLSLPAAQQ------PWHWLGSLY-LSKQGIYLPWPQTPG-------- 178 +L+ +I+ + + +P ++ L L+ + +G+Y+P P Sbjct: 140 VLIWIIIIFTIMTAVMPGPREFRGDNATSSMLFDLFAFTNRGVYIPMPWFESGFFASGAL 199 Query: 179 -WLVVILAIALVLFVSWLAQRQRS---------PRDWRWLYGAIAVVTVLMLLTQ-LSWP 227 WLVVI A+ V + + P+ G V L+L LSW Sbjct: 200 NWLVVIAALVGSFLVMRRIEANATKTQEKTGVRPKTKLIALGVWLVPLALVLFVMGLSWE 259 Query: 228 -QQLQPGQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTR 286 +L+ +GG+++ AL L YTGAFI E +R GI ++ GQ EAAAALGL Sbjct: 260 VPELKGFNFKGGIKIGGPLIALWFALSIYTGAFIAENVRAGIQAINKGQTEAAAALGLRP 319 Query: 287 SQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTLNQTGRPVEV 345 + + +V+PQALRVI+P L S ++ KNSSLAIAVGY D+ AT TLNQTGR +E Sbjct: 320 GRIMNLVVLPQALRVIIPPLISNFLNITKNSSLAIAVGYADITATLGGITLNQTGRAIEC 379 Query: 346 FLILMLTYLAINAVISAGMN 365 L+LML YL + +IS MN Sbjct: 380 VLLLMLFYLTASLLISMVMN 399 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: 386 Number of extensions: 19 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: 410 Length adjustment: 31 Effective length of query: 346 Effective length of database: 379 Effective search space: 131134 Effective search space used: 131134 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