Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate AO353_07795 AO353_07795 beta-aspartyl peptidase
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__pseudo3_N2E3:AO353_07795 Length = 665 Score = 347 bits (889), Expect = 1e-99 Identities = 182/526 (34%), Positives = 298/526 (56%), Gaps = 30/526 (5%) Query: 32 LKVGPFGLDIHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGN 91 +K P + ++ VF S I+L + Q+ +AWL + W+++ Sbjct: 7 IKTPPEKVTVNGWVFYTSTALILLLTAILIAAPQEAGRMLGIAQAWLSRSFGWYYMVVIA 66 Query: 92 VFVIVCLVLIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSS 151 +++ + L + G++++G + TPD+SY W MLF++G+GI L++FG SEP+ H+ + Sbjct: 67 AYLVFVVGLAFSSYGKLKLGSKDDTPDFSYGAWAGMLFSSGIGISLLYFGASEPLDHYFN 126 Query: 152 ALGGVNIENGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSF 211 P GA G ++ A+ + T HW LH W+IYAL+ L +A F++ Sbjct: 127 ----------------PPEGAAG-SNLAARQAVQLTFLHWGLHGWAIYALVGLAVAYFAY 169 Query: 212 NKGLPLTMRSIFYPLFGER-VWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLF 270 PL +RS YPL GER V G GH +D + T+ GL T+LG G+ Q ++GL LF Sbjct: 170 RHNQPLALRSALYPLVGERWVKGAAGHAVDGFGMFVTLLGLVTNLGIGSLQVSSGLENLF 229 Query: 271 GVPMTDTTQVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAIL 330 G+ +DT +++I+V++ +A I+ V+G+++G++RLS +N++L + LL FV++ GPT+ +L Sbjct: 230 GMAHSDTNLLIVIIVMSTVATIAAVSGVENGIRRLSNLNIVLFSGLLIFVLLFGPTLHLL 289 Query: 331 TGFFDNIASYITNIPALSMPFEREDVNYSQG------WTAFYWAWWISWSPFVGMFIARV 384 GF NI Y+ + + + + ++ WT FYWAWWISW+PFVGMFIAR+ Sbjct: 290 NGFVQNIGDYLNGVVLKTFDLYVYEADNAKSERWLGLWTLFYWAWWISWAPFVGMFIARI 349 Query: 385 SRGRSVREFIICVILIPSTVCVLWMTAFGGTAISQYVNDGYEAVFNAEL---PLKLFAML 441 SRGR+VRE + V+LIP + W++ FG +A+ +N G + L + ++ +L Sbjct: 350 SRGRTVRELVAGVLLIPLGFTLAWLSIFGNSALDLVMNHGAVELGKTALEQPSMAIYQLL 409 Query: 442 DVMPFAEITSVVGIILVVVFFITSSDSGSLVIDTIAA-GGKVDAPTPQ--RVFWCTFEGL 498 + P ++I V I + V F+T +DSG++++ ++ GG VD P R+FW L Sbjct: 410 EHYPASKIVIGVSIFVGFVLFLTPADSGAVMMANLSCKGGNVDEDAPHWLRIFWSVVITL 469 Query: 499 VAIALMLGGGLAAAQAMAVTTGLPFTIVLLVATVSLIKGLMDEPRL 544 V I L+L G A Q M V GLPF++VL+ L K + + ++ Sbjct: 470 VTIGLLLAGNFEAMQTMVVLAGLPFSVVLVFFMFGLHKAMRQDVQI 515 Lambda K H 0.327 0.141 0.435 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: 923 Number of extensions: 55 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: 553 Length of database: 665 Length adjustment: 37 Effective length of query: 516 Effective length of database: 628 Effective search space: 324048 Effective search space used: 324048 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: 53 (25.0 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