Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_057509185.1 ABB28_RS13885 BCCT family transporter
Query= SwissProt::G3XCN6 (706 letters) >NCBI__GCF_001431535.1:WP_057509185.1 Length = 525 Score = 402 bits (1034), Expect = e-116 Identities = 199/479 (41%), Positives = 305/479 (63%), Gaps = 2/479 (0%) Query: 57 VFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAFSR 116 VF S+A++A+ V + +AP S+ + ++ G GWLYLL V + L +L+LAF R Sbjct: 2 VFRISIALVAVLVLLAGLAPDAFNSVVQTVLAEVVRGAGWLYLLVVFLALSFLLYLAFGR 61 Query: 117 YGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEA-EPLTIAAQ 175 + L++G +D+EP+F SW++MLFAAGMGIGL+++ EP++HF PPE EP+ + A Sbjct: 62 FANLRIGGEDAEPDFSRASWMSMLFAAGMGIGLVFWGAAEPVSHFVKPPEGLEPMGMEAA 121 Query: 176 REAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGHVVD 235 R +M FFHWG+H WAIY+++GL++A+F + N V L P++ G IG VV+ Sbjct: 122 RASMRYAFFHWGLHPWAIYALIGLAMAWFQFNRNGRGLVSDMLQPIIGHHHRGWIGQVVN 181 Query: 236 IFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTGVEK 295 I A+ T G+AT+LGFG +QI +GL + GIP ++ Q++++ V + S ++GV++ Sbjct: 182 IAAVVATAIGVATTLGFGTIQIAAGLERVFGIPSNVPTQMVIIAVAFVLYMASTMSGVDR 241 Query: 296 GVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPRPWI 355 G++ LS NL LA LL+ VLV+GPTG + F +G YL+ LV + + + W+ Sbjct: 242 GIKWLSNFNLGLAALLLAMVLVLGPTGFIFDTFTTTLGSYLNQLVTMSLRMSPFSGSTWV 301 Query: 356 DSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTAIYV 415 WT+FYWAWWI+W+PFVG FIARISRGR+VREFV V+ P + F+W +VFG TA++ Sbjct: 302 VDWTIFYWAWWIAWAPFVGAFIARISRGRSVREFVVGVVIAPTVLGFIWFSVFGGTALW- 360 Query: 416 DTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVIDTI 475 + +L + LF F+ LP P V +++A++L+ IFFVTS+DS LV+ ++ Sbjct: 361 SQIFGHVDLVAALGNGYETVLFTMFDSLPLPLVLASVALVLLMIFFVTSADSAVLVLASM 420 Query: 476 ASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLILVWSLF 534 ++ P +++ W ++AA LL GGL ALQ ALPF+L+M++++ SL+ Sbjct: 421 STDEAGDPPLKRKVAWGVAIALIAAALLLAGGLAALQGMITIAALPFALLMILVMVSLY 479 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: 991 Number of extensions: 62 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: 706 Length of database: 525 Length adjustment: 37 Effective length of query: 669 Effective length of database: 488 Effective search space: 326472 Effective search space used: 326472 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 24 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