Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 138 bits (348), Expect = 4e-37 Identities = 80/230 (34%), Positives = 134/230 (58%), Gaps = 6/230 (2%) Query: 44 VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103 V + + GE ++G SG GK+T+ R + RLI+PT G+++ +G +I I LR++ Sbjct: 336 VDQLNFEVFPGETLGLVGESGCGKTTLGRTILRLIQPTSGEIIFNGENITHIGKTALRKL 395 Query: 104 RRKKIAMVFQS--FALMPHMTVLDNTAFGMELAGI--NAEERREKALDALRQVGL-ENYA 158 R K I ++FQ +L P +++ + +++ + N ER++K L+ L +VGL E + Sbjct: 396 R-KDIQIIFQDPYASLNPKLSIGQSILEPLQVHKLYRNDSERKQKVLELLDKVGLKEEHF 454 Query: 159 HSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTI 218 + YP E SGG RQRV +ARALA+ P ++ DE+ SALD ++ ++ + + LQ++ T Sbjct: 455 NRYPHEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQVLNLIKDLQSEFGLTY 514 Query: 219 VFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268 +FISHDL I DRI +M G++ + G P++I P Y + + Sbjct: 515 IFISHDLAVVKHISDRILVMNKGKIEEEGFPEQIFYAPKAAYTQKLIEAI 564 Score = 120 bits (300), Expect = 1e-31 Identities = 80/267 (29%), Positives = 135/267 (50%), Gaps = 24/267 (8%) Query: 36 EKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKS----TMVRLLNRLIEPTRGQVLIDGVD 91 EKT VK S +++G + I+G SGSGKS +++RL + G++ + + Sbjct: 16 EKTWFK-AVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDIS 74 Query: 92 IAKISDAELREVRRKKIAMVFQS--FALMPHMTVLDNTAFGMEL-AGINAEERREKALDA 148 + +S E+R++R +I+M+FQ +L P T A + L ++ E ++ + Sbjct: 75 LLNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKKHTIAL 134 Query: 149 LRQVGL---ENYAHSYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQD 205 +V L E SYP ++SGG +QRV +A AL+ +P +L+ DE +ALD ++ + Sbjct: 135 FNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQ 194 Query: 206 ELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF 265 L+KL+ + ++FISHDL I D +A+M GE+V+ G I NP + Y + Sbjct: 195 LLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIFENPQHPYTKGLL 254 Query: 266 RGVDISQVFSAKDIARRTPNGLIRKTP 292 R +PN ++K P Sbjct: 255 -------------ACRPSPNRQLKKLP 268 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: 491 Number of extensions: 24 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 568 Length adjustment: 33 Effective length of query: 367 Effective length of database: 535 Effective search space: 196345 Effective search space used: 196345 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: 51 (24.3 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