Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 181 bits (459), Expect = 3e-50 Identities = 89/239 (37%), Positives = 149/239 (62%), Gaps = 6/239 (2%) Query: 26 EQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQV 85 E + + ++++ G ++ V++ L IE GE+ ++G SG GK+T++R++ L PT+G + Sbjct: 42 EPAVRLQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDI 101 Query: 86 LIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKA 145 I G +I+D + ++ + M+FQ++AL PH T+ +N AFG++ ++ EE REK Sbjct: 102 YIKG---RRINDTP---IHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKV 155 Query: 146 LDALRQVGLENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQD 205 AL V L Y +LSGG +QR+ LARA+ I PD+LLMDE SALD +R EM+ Sbjct: 156 AQALEMVRLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRM 215 Query: 206 ELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264 E+ +Q + T +F++HD EA+ + ++I +M++G Q GTP+++ + P N +V F Sbjct: 216 EIDNIQQQLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADF 274 Lambda K H 0.319 0.137 0.378 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: 358 Number of extensions: 11 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: 400 Length of database: 406 Length adjustment: 31 Effective length of query: 369 Effective length of database: 375 Effective search space: 138375 Effective search space used: 138375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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