Align L-lysine transport protein (characterized)
to candidate BWI76_RS16225 BWI76_RS16225 arginine:ornithine antiporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__Koxy:BWI76_RS16225 Length = 460 Score = 301 bits (772), Expect = 2e-86 Identities = 166/476 (34%), Positives = 269/476 (56%), Gaps = 33/476 (6%) Query: 18 RTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLAR 77 + + + L AL++ S +GAG+FS+PQN+ +VA P A+LIGW I GVG+L +AF +L R Sbjct: 3 KKLGLSALTALVLSSMLGAGVFSLPQNMAAVASPSALLIGWGITGVGILFLAFAMLLLTR 62 Query: 78 RKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVP-----LF 132 +P LD G++ YAR G G+ +GF SAWGYWL +V+A V Y + FS L + LF Sbjct: 63 IRPDLDGGIFTYAREGFGELIGFCSAWGYWLCAVVANVSYLVIVFSALSFFTDTPELRLF 122 Query: 133 SQDHPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWE 192 + + S + S L W+V +V RG+ AA + T+AK+LPL FI L A + F E Sbjct: 123 GDGNTWQSIIGASVLLWIVHFLVLRGVQTAAGINLAATLAKLLPLGAFIALAA-MAFRME 181 Query: 193 KFTVDLWARDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVA 252 F +D GV +++QV+ M+ T+WVFIG+EGA V S +AR++ DV RAT++ ++ Sbjct: 182 TFRLDFSGLALGV-PVWEQVKNTMLITLWVFIGVEGAVVVSARARNKQDVGRATLLAVLS 240 Query: 253 VLLLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSW 312 L + + ++ LS GV+ + ELA + + SMA ++ ++G WG +I+ GL +SV GAY+SW Sbjct: 241 ALAVYLLVTLLSLGVVPRSELAEIRNPSMAGLMVNMMGSWGEIVIAAGLIISVCGAYLSW 300 Query: 313 QMLCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQ 372 ++ AE L A P N A + ++ I +Q +++ +L + Y +++ Sbjct: 301 TIMAAEVPYLAATHKAFPRLFARTNKNNAPSSSLWLTNISVQASLVLIWLTGSDYSTLLT 360 Query: 373 LATNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATV 432 +A+ + LVPY +L+ +A R H VG+ A + Sbjct: 361 IASEMILVPYFLVGAFLLKIARR-------------------------PLHKAVGVGACI 395 Query: 433 YSVWLFYAAEPQFVLFGAMAMLPGLIPYVWT-RIYRGEQVFNRFEIGVVVVLVVAA 487 Y +WL YA+ P +L + PGL+ +++ R ++ ++ R ++ ++ L+VAA Sbjct: 396 YGLWLLYASGPVHLLLSVILYAPGLLVFLYARRTHQHDRPLKRRDLALIGFLLVAA 451 Lambda K H 0.327 0.139 0.421 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: 642 Number of extensions: 33 Number of successful extensions: 4 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: 501 Length of database: 460 Length adjustment: 34 Effective length of query: 467 Effective length of database: 426 Effective search space: 198942 Effective search space used: 198942 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