Align L-glutamine and L-histidine transporter (characterized)
to candidate WP_085770386.1 B1812_RS03615 amino acid permease
Query= reanno::Korea:Ga0059261_1577 (470 letters) >NCBI__GCF_002117405.1:WP_085770386.1 Length = 488 Score = 315 bits (807), Expect = 2e-90 Identities = 180/463 (38%), Positives = 266/463 (57%), Gaps = 17/463 (3%) Query: 5 LFRTKRVKDAAEQAPEH-RLAATLSWPHLVALGVGAIVGTGILTLIGV-GAGKAGPAVIM 62 LFR K ++ +A E L L LV +G+G ++G GI L GV A +AGP V + Sbjct: 6 LFRAKSIESLQAEALERGALRRALGLWQLVGIGLGGLIGVGIFVLTGVVAATQAGPGVAL 65 Query: 63 SFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTV 122 SF+IAG AAL YAE A+M+P +GSAY Y+YAVLGE+ AW++GW L+LEY+LVV+ V Sbjct: 66 SFLIAGVASGAAALCYAEFASMLPVAGSAYTYAYAVLGELPAWIIGWDLLLEYALVVAVV 125 Query: 123 AVGWSGYAAPLLHAWTGMPLELMAGPHANG---IVNLPAIFIIAVVAGLLCLGTKESATL 179 ++GWSGY LL + P E AG G I++L A+ VA LL L + A Sbjct: 126 SIGWSGYLRALLALFGVAPPEWAAGAPGTGDGHILDLFAMLGAFGVALLLTLRVEWGARF 185 Query: 180 NAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAF 239 N A+V++KI A+ V + A P+ N AN PF PFGF GV+ AA++FFA Sbjct: 186 NTAMVLLKIAAVIVVILAAAPHINPANWRPFMPFGFG----------GVVEGAAVVFFAV 235 Query: 240 YGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLAL 299 +G+D ++TA EE P RDL ++ S++ + +Y+L+++A G + N+ P+A Sbjct: 236 FGYDTLTTAGEEALEPQRDLPRAVLLSLVVSLTLYILMSLALTGIARYDTLDNA-APVAS 294 Query: 300 ILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKR-GSP 358 LG ++ +A++ + +V+L FL G +RI+F M+RDG+LP A+ + +P Sbjct: 295 AFAALGMGWATLVVSAAAVVGILSVMLAFLLGCARIWFAMSRDGLLPAWFARPHPQFATP 354 Query: 359 VRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPL 418 R TL + A+++ PI E+A L N GTL+AF + + ++ LR PD+PR FR PL Sbjct: 355 YRPTLIAGGLCALVSAFFPIREVAELVNIGTLSAFVVICLAVIALRHTRPDVPRGFRAPL 414 Query: 419 WWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYAR 461 + I V ++L LP F+ W +G+ +YF Y R Sbjct: 415 SPYLPLIGVGFSLWLLSKLPAIAWERFVVWLIIGLAVYFLYGR 457 Lambda K H 0.327 0.140 0.426 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: 730 Number of extensions: 55 Number of successful extensions: 9 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: 470 Length of database: 488 Length adjustment: 34 Effective length of query: 436 Effective length of database: 454 Effective search space: 197944 Effective search space used: 197944 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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