Align L-glutamine and L-histidine transporter (characterized)
to candidate BPHYT_RS33230 BPHYT_RS33230 amino acid permease
Query= reanno::Korea:Ga0059261_1577 (470 letters) >FitnessBrowser__BFirm:BPHYT_RS33230 Length = 486 Score = 352 bits (902), Expect = e-101 Identities = 190/461 (41%), Positives = 276/461 (59%), Gaps = 16/461 (3%) Query: 14 AAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGK-AGPAVIMSFVIAGAICA 72 +A+ H L+ +L + A+G+GAI+G GI L G A + AGP++++SFV+ G CA Sbjct: 18 SADADEGHSLSKSLGAISITAMGIGAIIGAGIFVLTGTAAAQFAGPSIVLSFVLGGIACA 77 Query: 73 CAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVAVGWSGYAAP 132 L Y+E+A M+P GS+Y Y+YA LGEI AW++GW LILEY++ +TVAVGWSGY Sbjct: 78 FVGLCYSELAAMLPVCGSSYTYTYATLGEIFAWIIGWDLILEYAMGAATVAVGWSGYIVS 137 Query: 133 LLH-----------AWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLNA 181 LLH G ++L G A GIVNLPAI IIA++ +L LGTKESA LN Sbjct: 138 LLHNVGISIPPVLATAPGTVIKLADGTTATGIVNLPAIVIIAILTTMLVLGTKESARLNN 197 Query: 182 ALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFYG 241 +V VK++ + F+A+ + + AN PF P + G+ G++ +A++FFAF G Sbjct: 198 IMVAVKLVVVVAFIALGVFFIKPANWHPFIPANTGE-FGNFGMS-GILRGSAVVFFAFIG 255 Query: 242 FDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALIL 301 FDA+STAA+E K P RD+ IGI+GS+I C +Y+LVA G P+ N P+P+A + Sbjct: 256 FDAVSTAAQEAKKPQRDMPIGILGSLIICTILYILVAGVLTGLVPYAEL-NVPDPIAKGV 314 Query: 302 RDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKR-GSPVR 360 +G F+ + + A+ L TV+L L+GQSRIFFTM+ DG+LP A+V R +P Sbjct: 315 DAIGLNWFSILIKIGALTGLTTVILVLLYGQSRIFFTMSTDGLLPPLFARVHPRLQTPYL 374 Query: 361 ITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWW 420 + ++VA++A L PI + + + GTL AF V ++ LR D R FR P Sbjct: 375 SQILIGSVVAIVAALTPISVLGEMVSIGTLFAFILVCGAVIYLRRSDSDASRPFRVPGVP 434 Query: 421 LVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYAR 461 +V + +L C+ L LP+ T + + W +G+ IY +Y R Sbjct: 435 VVPVLGILFCLLLMAGLPLVTWVRLVVWLVIGMTIYMSYGR 475 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: 673 Number of extensions: 39 Number of successful extensions: 6 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: 486 Length adjustment: 34 Effective length of query: 436 Effective length of database: 452 Effective search space: 197072 Effective search space used: 197072 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