Align L-glutamine and L-histidine transporter (characterized)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__Pedo557:CA265_RS17395 Length = 483 Score = 305 bits (782), Expect = 2e-87 Identities = 168/469 (35%), Positives = 264/469 (56%), Gaps = 15/469 (3%) Query: 15 AEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AGPAVIMSFVIAGAICAC 73 A ++ E L TL +L+ +GVG +G G+ ++ G+ A +GPAV +SFVIA C Sbjct: 12 ANESGEGSLKRTLGPINLILIGVGLTLGAGLFSITGLAAANHSGPAVTLSFVIAALGCGF 71 Query: 74 AALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAPL 133 AAL YAE A+M+P +GSAY YSYA +GE+ AW++GW L+LEYS+ +TVA+ WS Y Sbjct: 72 AALCYAEFASMIPVAGSAYTYSYATMGELFAWIIGWDLVLEYSVGCATVAISWSQYLTKF 131 Query: 134 ---LHAW-----TGMPLE---LMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLNAA 182 LH + T P E L G NGI+N+PA ++ ++ +L GTK SA +N Sbjct: 132 LASLHIYLPPQLTLSPFETAKLADGSTVNGIINIPAALVVVLMTAILIRGTKGSAIVNGI 191 Query: 183 LVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFYGF 242 +V +K+ + VF+A+ Y + AN P+ P T G GV+ A ++FF F GF Sbjct: 192 IVFLKVGVVLVFIALGWQYIDPANYHPYIPEN-TGTFGQFGWS-GVLRGAGLVFFVFIGF 249 Query: 243 DAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALILR 302 DA++ +A+ETKNP RDL IGI+GS++ C ++ L G + FANS P+A+ + Sbjct: 250 DAVAASAQETKNPARDLPIGIIGSLLVCTVLFGLFGHVMTGLANYKEFANSGAPVAIAIE 309 Query: 303 DLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKV-SKRGSPVRI 361 + + ++ +I +V+L L QSR+F+++++DG+LP + V +K +P + Sbjct: 310 KTPYAWLSQAIILAILIGYTSVILIDLMAQSRMFYSISKDGLLPKMFSDVHAKFKTPYKS 369 Query: 362 TLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWWL 421 + + + A +P++ + + + GTL AF V V +++LR P+ R F+ P L Sbjct: 370 NIILCVFIGLFAAFVPMNVVGEMTSIGTLLAFLMVCVGILILRKTNPEAKRPFKVPFVPL 429 Query: 422 VGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYARPRVSAKGIE 470 + + +L CI + LP +T L W +G+ IYF Y + K E Sbjct: 430 IPILGILTCIAMMVFLPWETWLRLAVWLIIGLAIYFWYGKKNSKLKAQE 478 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: 653 Number of extensions: 26 Number of successful extensions: 5 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: 483 Length adjustment: 33 Effective length of query: 437 Effective length of database: 450 Effective search space: 196650 Effective search space used: 196650 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 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