Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 211 bits (536), Expect = 4e-59 Identities = 143/389 (36%), Positives = 207/389 (53%), Gaps = 48/389 (12%) Query: 29 QIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYSNDDTHFRAL 88 Q++VLL+ G +WL++N NL +G +F +L AG+++ ++ I Y D++ RAL Sbjct: 23 QLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSYARAL 82 Query: 89 IEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIPLLLWILLMG 148 + GL+N+L V +G IL T++GT+ GV S+NWL+ ++ YV RN PLLL +++ Sbjct: 83 VVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWY 142 Query: 149 TILAETRPVPKDFRLTEAMKAAGEEPKASMW-FFDSVAVTNRGTNLPAPAFDHSLGVVDL 207 + + P A ++P W + S+ ++ +G LP P Sbjct: 143 FPILLSLP-------------AAQQP----WHWLGSLYLSKQGIYLPWPQTP-------- 177 Query: 208 GWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWWPSLLILFAPISALL 267 GW + ILA+ F W A R W L A ++ L+ Sbjct: 178 GW-------LVVILAIALVLFVSWL-----------AQRQRSPRDWRWLYGAIAVVTVLM 219 Query: 268 YGLGFHLDYPQ-ITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTE 326 L L +PQ + GG ++ FTALL+ L YT AFI EI+R GI ++ GQ E Sbjct: 220 --LLTQLSWPQQLQPGQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWE 277 Query: 327 AAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITL 386 AA ALGL +T+ +++PQALRVIVP L SQ++ KNSSLAIAV Y DL T TL Sbjct: 278 AAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYAT-AQTTL 336 Query: 387 NQTGRELECMLLMMLIYLTISLTISSLMN 415 NQTGR +E L++ML YL I+ IS+ MN Sbjct: 337 NQTGRPVEVFLILMLTYLAINAVISAGMN 365 Lambda K H 0.326 0.139 0.419 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: 374 Number of extensions: 13 Number of successful extensions: 3 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: 426 Length of database: 377 Length adjustment: 31 Effective length of query: 395 Effective length of database: 346 Effective search space: 136670 Effective search space used: 136670 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: 50 (23.9 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