Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate AZOBR_RS23220 AZOBR_RS23220 beta-aspartyl peptidase
Query= SwissProt::Q87NZ5 (553 letters) >FitnessBrowser__azobra:AZOBR_RS23220 Length = 662 Score = 414 bits (1063), Expect = e-120 Identities = 215/508 (42%), Positives = 303/508 (59%), Gaps = 24/508 (4%) Query: 41 IHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVFVIVCLVL 100 I+ V +G IVLFV+ F + + L++ +V N WF++ S F++ L Sbjct: 4 INKTVSFTAGGLIVLFVLLASVFTEPFGERISALQSAIVGNFGWFYILSVAGFLLFAFWL 63 Query: 101 IVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSSALGGVNIEN 160 +P G +++G + P++SY W AMLF+AGMGIGL+F+GV+EP+ H ++ Sbjct: 64 FFSPYGSIKLGKDDDEPEFSYLTWFAMLFSAGMGIGLLFYGVAEPVLHLAN--------- 114 Query: 161 GVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSFNKGLPLTMR 220 P G G DAA M HW LH W IY + L L F++ LPLT+R Sbjct: 115 -------PRVGEAGTPDAARE-AMNLAFLHWGLHAWGIYITVGLSLGYFAYRHDLPLTIR 166 Query: 221 SIFYPLFGERVWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLFGVPMTDTTQV 280 S YPL G+R+ GW GH++DI+A+V T+FG+ATSLG G Q GL++L V + Q+ Sbjct: 167 SALYPLLGDRLSGWPGHLVDIVAIVGTLFGIATSLGLGVMQINAGLDYLGLVSVGTVQQM 226 Query: 281 VLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAILTGFFDNIASY 340 VLI VITA+A S V+G+ G++RLSE+NM+ +LL FV ++GP++ +L+ ++I Y Sbjct: 227 VLIAVITAIATASAVSGVGRGIRRLSELNMLAGLLLLLFVFLLGPSVFLLSTLVESIGRY 286 Query: 341 ITNIPALS---MPFEREDVNYSQGWTAFYWAWWISWSPFVGMFIARVSRGRSVREFIICV 397 + +P S +P+ + WT FYW WWISW+PFVGMFIARVSRGR++REFI V Sbjct: 287 LWTLPYTSFRTLPY--TGAEWQASWTMFYWGWWISWAPFVGMFIARVSRGRTIREFIGGV 344 Query: 398 ILIPSTVCVLWMTAFGGTAI--SQYVNDGYEAVFNAELPLKLFAMLDVMPFAEITSVVGI 455 + P + +W T FG TAI + G A +P LF MLD +P + ITS + Sbjct: 345 LFAPVALTFVWFTVFGETAIHMEMFEGGGMAAAVQENVPTALFVMLDRLPLSVITSALAT 404 Query: 456 ILVVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTFEGLVAIALMLGGGLAAAQAM 515 ++VV FF+TS+DSG+LVID I +GG D P R+FW G+VA L+L GGL A Q Sbjct: 405 LIVVTFFVTSADSGALVIDIIGSGGNQDPPIATRIFWAVLCGVVAAVLLLVGGLQALQTA 464 Query: 516 AVTTGLPFTIVLLVATVSLIKGLMDEPR 543 AVTT LPF +V+++ V L+ L E R Sbjct: 465 AVTTALPFAVVMVLMCVGLVTSLRAERR 492 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: 1009 Number of extensions: 55 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: 553 Length of database: 662 Length adjustment: 37 Effective length of query: 516 Effective length of database: 625 Effective search space: 322500 Effective search space used: 322500 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