Align lysine-specific permease (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP
Query= CharProtDB::CH_091040 (611 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559 Length = 473 Score = 240 bits (613), Expect = 9e-68 Identities = 146/440 (33%), Positives = 231/440 (52%), Gaps = 21/440 (4%) Query: 106 VKRALKQRHIGMIALGGTIGTGLFVGISTPLSNAGPVGSLIAYIFMGTIVYFVTQSLGEM 165 +KR LK RHI +IALGG IGTGLF+G + L +AGP ++ Y G I + + + LGEM Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAICGFIAFMIMRQLGEM 69 Query: 166 ATFIPVTSSITVFSKRFLSPAFGVSNGYMYWFNWAITYAVEVSVIGQVIEYWTDKVPLAA 225 PV S + F+ ++ G +G+ W + + E++ +G+ I YW +P Sbjct: 70 IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWV 129 Query: 226 WIAIFWVIITLMNFFPVKVYGEFEFWVASVKVLAIMGYL-IYALIIVCGGSHQGPIGFRY 284 A F+V+I L+N VKV+GE EFW A +KV+AI+G + + + ++V G Sbjct: 130 SAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGDGGPQASVTNL 189 Query: 285 WRNPGAWGPGIISSDKSEGRFLGWVSSLINAAFTYQGTELVGITAGEAANPRKTVPRAIN 344 W + G + G+ G V ++ F++ G E++G TA EA P+ +P+AIN Sbjct: 190 WEHGGFFPNGV----------SGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAIN 239 Query: 345 KVVFRIVLFYIMSLFFIGLLVPYND--SRLSASSAVIASSPFVISIQNAGTYALPDIFNA 402 +V++RI++FYI +L + L P++ + L+AS + SPFV G+ I N Sbjct: 240 QVIYRILIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNF 299 Query: 403 VVLITVVSAANSNVYVGSRVLYSLARTGNAPKQFGYVTRQGVPYLGVVCTAALGLLAFLV 462 VVL +S NS Y SR+L +A G+APK + ++GVP ++ +AA+ L+A L+ Sbjct: 300 VVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLL 359 Query: 463 VNNNANTAFNWLINISTLAGLCAWLFISLAHIRFMQALKHRGISRDDLPFKAKLMPYGAY 522 A L+++ + W IS +H +F Q H ++ FKA PYG Y Sbjct: 360 NYLVPQHALELLMSLVVATLVINWAMISFSHFKFRQ---HMNKTKQTPLFKALWYPYGNY 416 Query: 523 ----YAAFFVTVIIFIQGFQ 538 + F + V++ I G Q Sbjct: 417 VCLAFVVFILGVMLLIPGIQ 436 Lambda K H 0.324 0.138 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: 707 Number of extensions: 35 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: 611 Length of database: 473 Length adjustment: 35 Effective length of query: 576 Effective length of database: 438 Effective search space: 252288 Effective search space used: 252288 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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