Align L-lysine transport protein (characterized)
to candidate AZOBR_RS13260 AZOBR_RS13260 amino acid APC transporter
Query= CharProtDB::CH_019644 (501 letters) >FitnessBrowser__azobra:AZOBR_RS13260 Length = 480 Score = 397 bits (1021), Expect = e-115 Identities = 205/476 (43%), Positives = 292/476 (61%), Gaps = 22/476 (4%) Query: 17 SRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHVLA 76 S +++ L+AL++GS +G G+F++P ++ A PGA+LIGW+I G+GM+ +AFV+ LA Sbjct: 7 SDKLTLLPLVALVVGSMIGGGVFNLPSDMSKGASPGAILIGWMITGIGMMMLAFVYQNLA 66 Query: 77 RRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQDH 136 RKP+L++G YAYA+ G G +VGF+SAWGYWL + + V YA FS L H+ P+F + Sbjct: 67 VRKPNLNAGPYAYAKAGFGPFVGFNSAWGYWLSAFLGNVAYAVAIFSALSHFFPIFGDGN 126 Query: 137 PFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLGFSWEKFTV 196 S + S WL+ +V GI QAAF+ VT++AK++PL F+ LVA +GF W++FTV Sbjct: 127 NLPSIVGASLCLWLIHALVLSGIKQAAFVNVVTSIAKLVPLFLFV-LVAIVGFHWDRFTV 185 Query: 197 DLWARD-----GGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFV 251 D W GG+GS+ +QV+ M+ T+WVFIGIEGASVYS +A RSDV RATVIGFV Sbjct: 186 DFWGTGAGSGTGGLGSVMEQVKSTMLVTLWVFIGIEGASVYSARAARRSDVGRATVIGFV 245 Query: 252 AVLLLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVS 311 L + V +S L+ GVL Q ELA L SMA V E++VGPWGAALI++GL +SV GA++S Sbjct: 246 GALGIYVLVSLLATGVLRQPELADLKVPSMAGVFESLVGPWGAALINIGLVISVGGAFLS 305 Query: 312 WQMLCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMV 371 W +LCAE DG P A N+ G+ A + ++IQ+F+ + F + + Y Sbjct: 306 WTLLCAEIPYTCGRDGTFPKWFAAENANGSPVNALWATNLLIQLFLALSFFSRSAYQFFY 365 Query: 372 QLATNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVAT 431 +A+ L PY+ S Y + LA G+G K ++VG +AT Sbjct: 366 FIASVAILPPYVLSGAYALKLALTGEG----------------YGAESRTKGILVGALAT 409 Query: 432 VYSVWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAA 487 Y +WL YAA Q++L A+ PG++ YV R GE+ F E+ + + V A Sbjct: 410 AYGLWLVYAAGLQYLLMCAVLFAPGILVYVRARREHGERTFTGVEMAIAAAIAVLA 465 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: 779 Number of extensions: 50 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: 480 Length adjustment: 34 Effective length of query: 467 Effective length of database: 446 Effective search space: 208282 Effective search space used: 208282 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