Align Trehalose-binding lipoprotein LpqY (characterized)
to candidate Synpcc7942_0950 Synpcc7942_0950 putative multiple sugar transport system substrate-binding protein
Query= SwissProt::P9WGU9 (468 letters) >FitnessBrowser__SynE:Synpcc7942_0950 Length = 438 Score = 132 bits (332), Expect = 2e-35 Identities = 121/427 (28%), Positives = 174/427 (40%), Gaps = 62/427 (14%) Query: 45 ATFTAIAQRCNQQFGGRFTIAQVSLPRSPNEQRL----QLARRLTGNDRTLDVMALDVVW 100 A F Q +F Q+ L PN+ L L GN D++ LDV W Sbjct: 54 APFREAMQPAIARFTAEHPEIQLELVAGPNDTSLVSDLYTTAFLLGN-APYDLVFLDVTW 112 Query: 101 TAEFAEAGWALPLSDDPAGLAENDAVADTLPGPLATAGWNHKLYAAPVTTNTQLLWYRPD 160 +F AGW L LSD + A+ LP L + + +LY P+ LL+YR D Sbjct: 113 LPKFVAAGWLLDLSDRVLP----EIQAEFLPAALNGSFYRDRLYRLPLNAAVGLLYYRQD 168 Query: 161 LVNSPPTDWNAMIAEAARLHAAGEPSWIAV-QANQGEGLVVWFNTLLVSAGGSVLSEDGR 219 L+ PP + ++ + +L A G W V Q Q EGLV F +L GG + Sbjct: 169 LMPEPPQTFTELVQRSQQLQAQGVVPWGYVWQGKQYEGLVCNFLEVLAGFGGYWIDPQTG 228 Query: 220 HVTLTDTPAHRAATVSALQILKSVATTPGADPSITRTEEGSARLAFEQGKAALEVNWPFV 279 V L A ++A L S T + ++ +E A FE G++A NWP Sbjct: 229 EVGLDHPEA-----IAAADWLHSTITDQISPAGVSTFQENEALKLFETGQSAFMRNWP-- 281 Query: 280 FASML----ENAVKGGVPFLPLNRIPQLAGSINDIGTFTPSDEQFRIAYDASQQVFGFAP 335 +A ML E+AV+G V P+ Sbjct: 282 YAEMLLERPESAVRGKVGIAPM-------------------------------------- 303 Query: 336 YPAVAPGQPAKVTIGGLNLAVAKTTRHRAEAFEAVRCLRDQHNQRYVSLEGGLPAVRASL 395 APGQ + T G + +A+ T H A A+ L D +QR +SL R++L Sbjct: 304 --VHAPGQTSAATQGTWGVGIAQQTEHPEAALTALLALTDAESQRLISLGSNYIPTRSAL 361 Query: 396 YSDPQFQAKYPMHAIIRQQLTDAAVRPATPVYQALSIRLAAVLS-PITEIDPESTADELA 454 Y DP+ A+YP +A + L +R P Y ALS L LS I+ P + A + A Sbjct: 362 YQDPELLARYPFYATLPPILESTVLRSPLPAYDALSDILQRHLSAAISGQTPVAIALQQA 421 Query: 455 AQAQKAI 461 A+ + + Sbjct: 422 ARESRQL 428 Lambda K H 0.318 0.131 0.389 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: 472 Number of extensions: 26 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 468 Length of database: 438 Length adjustment: 33 Effective length of query: 435 Effective length of database: 405 Effective search space: 176175 Effective search space used: 176175 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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