Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like
Query= reanno::Smeli:SM_b21653 (298 letters) >FitnessBrowser__SynE:Synpcc7942_0526 Length = 293 Score = 171 bits (433), Expect = 2e-47 Identities = 97/277 (35%), Positives = 155/277 (55%), Gaps = 8/277 (2%) Query: 17 WLFVAPALGLITLFMVYPIAWSLWMSFQS---GRGMTLKFAGFANIVRLWNDPVFIKALT 73 +LF+APAL ++ L + +P + + SF + ++ G N RL ND VF K L Sbjct: 11 YLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDAVFWKTLG 70 Query: 74 NTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLPCVSSLVAYSVLFKGMFAT 133 NT Y + VP+++ L L LA L+N P L G +FR A + P + S+V + ++ ++A Sbjct: 71 NTFIYLIGVVPLLVFLPLGLAILVNRP-LRGITLFRLAYYTPVIVSIVVAGIAWRWLYAE 129 Query: 134 DGIVNSTLQAI-GLAASPIPWLTHPFWAKVLVILAITWRWTGYNMIFYLAALQNIDKSIY 192 G++N Q + G PIPWLT P A V+ W+ GY M+ YLA LQ I +Y Sbjct: 130 TGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVIYLAGLQGIPLELY 189 Query: 193 EVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDEVYNLTEGKGGPSNATLT 252 E A +DG W R +T+PL++P ++ VIS I ++F+EV+ +T+ GGP N++ T Sbjct: 190 EAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVFIMTQ--GGPLNSSKT 247 Query: 253 LSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQ 289 + Y+Y F+ + + YA TV + ++V L+ ++ Sbjct: 248 VVYYVYQQAFQKL-EVSYACTVGLALFLVVLTLSLLR 283 Lambda K H 0.330 0.142 0.447 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: 280 Number of extensions: 16 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: 298 Length of database: 293 Length adjustment: 26 Effective length of query: 272 Effective length of database: 267 Effective search space: 72624 Effective search space used: 72624 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 (21.9 bits) S2: 48 (23.1 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