Align L-glutamine and L-histidine transporter (characterized)
to candidate Ga0059261_1053 Ga0059261_1053 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Korea:Ga0059261_1053 Length = 512 Score = 410 bits (1055), Expect = e-119 Identities = 226/489 (46%), Positives = 308/489 (62%), Gaps = 44/489 (8%) Query: 7 RTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAVIMSFVI 66 R K + A + L +L L LG+GA++GTGI L A KAGP +++SFVI Sbjct: 5 RVKPLDAILATAEKKSLHRSLGAFQLTMLGIGAVIGTGIFVLTAEAAQKAGPGMMLSFVI 64 Query: 67 AGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGW 126 AG +CA AAL YAEMA M+P SGSAY YSYAV+GE+IAW+VGW+LILEY++ V+VGW Sbjct: 65 AGVVCAVAALCYAEMAAMVPVSGSAYTYSYAVMGELIAWMVGWALILEYAVAAGAVSVGW 124 Query: 127 SGYAAPLLHAWTGM--PLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLNAALV 184 SGY L+ + P L+ GP+ GI+NLPA+ I +V LL +GTKESA +N+ LV Sbjct: 125 SGYVVGLIENAFALDIPDALVRGPYDGGIINLPAMLIAGLVTWLLVIGTKESAFVNSVLV 184 Query: 185 VVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFYGFDA 244 +VK+ AL++F+ +A+P N N EPF+P GFA GV AAAA IFFA+ GFDA Sbjct: 185 LVKVSALSLFIILAIPVMNMQNFEPFSPLGFA----------GVSAAAASIFFAYVGFDA 234 Query: 245 ISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVA---VAAVGATPF-------------- 287 +STAAEETKNP R++ IG++GS+ C Y+LVA + +VGA P Sbjct: 235 VSTAAEETKNPQRNMPIGLIGSLAICTIFYLLVAAGVIGSVGAQPILGPDGAALPPGSTE 294 Query: 288 -------THFAN-------SPEPLALILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQS 333 T A S E LA LR++G P + ++A +ALP+V+L +FGQ+ Sbjct: 295 LTKACVETAAATGKEAVVCSKEALAWTLREIGWPQIGNLIGLAAGLALPSVILMMMFGQT 354 Query: 334 RIFFTMARDGMLPIGLAKVS-KRGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAA 392 RIFF M+RDG+LP +KV K +P IT+ T VA+ A P+ ++A ++N+GTL A Sbjct: 355 RIFFVMSRDGLLPAVFSKVHPKFHTPHVITILTGVFVALFAAFFPVGKLADISNSGTLFA 414 Query: 393 FTAVAVCMMVLRVRAPDMPRMFRTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALG 452 F AV++ ++VLR PD R FRTPL + IA+LGC YLF+SL T++ F+ W ALG Sbjct: 415 FAAVSIAVLVLRRTDPDRKRPFRTPLIIITAPIAILGCAYLFYSLGHDTKMMFVGWAALG 474 Query: 453 VVIYFAYAR 461 +++YF Y+R Sbjct: 475 LLVYFGYSR 483 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: 718 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 470 Length of database: 512 Length adjustment: 34 Effective length of query: 436 Effective length of database: 478 Effective search space: 208408 Effective search space used: 208408 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: 52 (24.6 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