Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate AZOBR_RS23220 AZOBR_RS23220 beta-aspartyl peptidase
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__azobra:AZOBR_RS23220 Length = 662 Score = 528 bits (1361), Expect = e-154 Identities = 284/627 (45%), Positives = 385/627 (61%), Gaps = 28/627 (4%) Query: 53 VNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFL 112 +N V + +I LFV + + + S +Q+AI+ FGW Y+LSVA FL +L Sbjct: 4 INKTVSFTAGGLIVLFVLLASVFTEPFGERISALQSAIVGNFGWFYILSVAGFLLFAFWL 63 Query: 113 AFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTI 172 FS YG +KLG DD EPEF YL+W AMLF+AGMGIGL+++ V EP+ H A+P E T Sbjct: 64 FFSPYGSIKLGKDDDEPEFSYLTWFAMLFSAGMGIGLLFYGVAEPVLHLANPRVGEAGTP 123 Query: 173 AAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGH 232 A REAM++ F HWG+HAW IY VGLSL YF YR++LPLT+RS LYPLL + + G GH Sbjct: 124 DAAREAMNLAFLHWGLHAWGIYITVGLSLGYFAYRHDLPLTIRSALYPLLGDRLSGWPGH 183 Query: 233 VVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTG 292 +VDI AI GT+FG+ATSLG G++QIN+GL+YL + Q++L+ V+TAIAT S V+G Sbjct: 184 LVDIVAIVGTLFGIATSLGLGVMQINAGLDYLGLVSVGTVQQMVLIAVITAIATASAVSG 243 Query: 293 VEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPR 352 V +G+R LSE N+ +LL+LFV ++GP+ L+ V++IG YL +L +F Y Sbjct: 244 VGRGIRRLSELNMLAGLLLLLFVFLLGPSVFLLSTLVESIGRYLWTLPYTSFRTLPYTGA 303 Query: 353 PWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTA 412 W SWT+FYW WWISW+PFVGMFIAR+SRGRT+REF+ VLF P TF+W TVFG TA Sbjct: 304 EWQASWTMFYWGWWISWAPFVGMFIARVSRGRTIREFIGGVLFAPVALTFVWFTVFGETA 363 Query: 413 IYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVI 472 I+++ G +A V+ ++ ALF + LP +TS LA L+V FFVTS+DSG+LVI Sbjct: 364 IHME-MFEGGGMAAAVQENVPTALFVMLDRLPLSVITSALATLIVVTFFVTSADSGALVI 422 Query: 473 DTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILVWS 532 D I SGG P RIFW L G+VAAVLL GGL ALQ+A ++TALPF++VM+++ Sbjct: 423 DIIGSGGNQDPPIATRIFWAVLCGVVAAVLLLVGGLQALQTAAVTTALPFAVVMVLMCVG 482 Query: 533 LFVGMRAD--------LARTQSPGSLGPRAYPASGVPWQRRLAMTL-------------S 571 L +RA+ +AR + G P W+++LA + Sbjct: 483 LVTSLRAERRAGPDRRVARVPTASEGGAPVQPVGDGDWRQQLAAVIGRKAAIAAAVPPGG 542 Query: 572 TPDRRAVEKFLQASVLPALEAVARELTRRSRPASVGRDAETGALT--LTVPAEGHRDFVY 629 RR V +F+ +V PA +A EL R R A + E G L V +G +F Y Sbjct: 543 AGARREVARFIADTVEPAFRDIAAELERLGRRAVI----EVGPFNAGLAVLRDGEEEFSY 598 Query: 630 GVQMSEHKLPAFTAYDATVADVRYEAR 656 ++ + F D AD +++ R Sbjct: 599 DIRARAYHPLTFAFPDLKAADEQWQMR 625 Lambda K H 0.326 0.139 0.422 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: 1329 Number of extensions: 77 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: 706 Length of database: 662 Length adjustment: 39 Effective length of query: 667 Effective length of database: 623 Effective search space: 415541 Effective search space used: 415541 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: 54 (25.4 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