Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::Smeli:SMc02119 (397 letters) >FitnessBrowser__Dino:3606889 Length = 411 Score = 309 bits (791), Expect = 1e-88 Identities = 178/398 (44%), Positives = 236/398 (59%), Gaps = 9/398 (2%) Query: 9 PERSRSSGSIINDPQVRGIFYQAITIIILAALIYWIVDNTVDNLRRANIASGYDFVRSRA 68 P + + G +IND + RG +Q I +I L W+V N + NL + F+ A Sbjct: 14 PNQPFNLGMLINDTRYRGYTFQFIALIALIFFFGWLVSNAIYNLAALGQDINFSFLGQPA 73 Query: 69 GFDVGQSLISFTSDSTYGRALLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKL 128 +++ Q+LI +TS T+ RA VG +NTLLVA G ITATI G + G+ RLS NW++AK+ Sbjct: 74 SYEIDQTLIPYTSTDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWLVAKV 133 Query: 129 SLAYVEVFRNIPPLLVIFFWYSGVLSILPQAR-----DALA---LPFDIFLSNRGVAFPR 180 YVE+FRNIP L+ I + + LPQ R DA A L + +NRGV P Sbjct: 134 MSVYVEIFRNIPVLIWIVIISAVMSQALPQPRAFRGEDATATMVLWDSVAFTNRGVYIPA 193 Query: 181 PIAEEGAEYTLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLGLIIGLPLVTFLVT 240 P+ G+ + FV+++ F RYA+ TG+ LPV L + L+ F V Sbjct: 194 PVWNPGSGIVVAVFVLSIIGIFVFRRYAKNLLFNTGKLLPVGRISLAIFFVPTLLAFFVM 253 Query: 241 GAPITFDIPVAGKFNLTGGSVVGPEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAA 300 G PI D P G FN GG + ++L+ AL+ YT AFIAE VRAGI VSKGQTEAA Sbjct: 254 GRPIGLDYPELGGFNFRGGINIRGTLIALWFALALYTGAFIAENVRAGILAVSKGQTEAA 313 Query: 301 HALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLV-AVGGTILNQ 359 ALG+RP L+++PQA+R+IIPP+ SQYLNLTKNSSLA AIGY DL +GG LNQ Sbjct: 314 AALGMRPNRIMSLIILPQALRVIIPPVISQYLNLTKNSSLAAAIGYMDLTGTLGGVTLNQ 373 Query: 360 TGQSIEIVSIWLIVYLSLSLATSLFMNWYNARMALVER 397 TG+S E V + ++ YL +SL+ S MN YN + L ER Sbjct: 374 TGRSFECVLLLMLFYLLISLSISALMNLYNNAVKLKER 411 Lambda K H 0.327 0.141 0.412 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: 427 Number of extensions: 13 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: 397 Length of database: 411 Length adjustment: 31 Effective length of query: 366 Effective length of database: 380 Effective search space: 139080 Effective search space used: 139080 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