Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= CharProtDB::CH_011913 (426 letters) >FitnessBrowser__Dino:3606889 Length = 411 Score = 415 bits (1066), Expect = e-120 Identities = 226/425 (53%), Positives = 290/425 (68%), Gaps = 25/425 (5%) Query: 4 ASDPPKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFL 63 AS PP F L MLI DTR+R T Q + L+ + WL++NA NL A G+D NFSFL Sbjct: 10 ASGPPNQPFNLGMLINDTRYRGYTFQFIALIALIFFFGWLVSNAIYNLAALGQDINFSFL 69 Query: 64 WTRAGYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWL 123 A Y++ QTLIPY++ DTH RA GLLNTLLV+ LGCI ATI G + GVLRLS+NWL Sbjct: 70 GQPASYEIDQTLIPYTSTDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWL 129 Query: 124 VARIMTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDS 183 VA++M+VYVE FRNIP+L+WI+++ ++++ P P+ FR GE+ A+M +DS Sbjct: 130 VAKVMSVYVEIFRNIPVLIWIVIISAVMSQALPQPRAFR--------GEDATATMVLWDS 181 Query: 184 VAVTNRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQE 243 VA TNRG +PAP ++ G+V V++ L+I+ + +RR+ AK + Sbjct: 182 VAFTNRGVYIPAPVWNPGSGIV-------VAVFVLSIIGIFV-----FRRY---AKNLLF 226 Query: 244 ATGTRPTTWWPSLLILFAPISALLYGLG--FHLDYPQITKFDFTGGFQMLHSFTALLIAL 301 TG SL I F P + +G LDYP++ F+F GG + + AL AL Sbjct: 227 NTGKLLPVGRISLAIFFVPTLLAFFVMGRPIGLDYPELGGFNFRGGINIRGTLIALWFAL 286 Query: 302 TLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLN 361 LYT AFIAE VRAGI A+S+GQTEAA ALG+RP R MSL+ILPQALRVI+PP+ISQ+LN Sbjct: 287 ALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMSLIILPQALRVIIPPVISQYLN 346 Query: 362 LTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSI 421 LTKNSSLA A+ YMDL GTLGG+TLNQTGR EC+LL+ML YL ISL+IS+LMNLYN ++ Sbjct: 347 LTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLMLFYLLISLSISALMNLYNNAV 406 Query: 422 KLKER 426 KLKER Sbjct: 407 KLKER 411 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: 500 Number of extensions: 19 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: 411 Length adjustment: 32 Effective length of query: 394 Effective length of database: 379 Effective search space: 149326 Effective search space used: 149326 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