Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 137 bits (345), Expect = 5e-37 Identities = 81/216 (37%), Positives = 133/216 (61%), Gaps = 9/216 (4%) Query: 30 EIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDLSGAKIDQKHLRQLRVRV 89 E++P + + ++G SGCGK+T R + RL + G + G +++ I + LR+LR + Sbjct: 342 EVFPGETLGLVGESGCGKTTLGRTILRLIQPTSGEIIFNGENIT--HIGKTALRKLRKDI 399 Query: 90 GMVFQ--HFNLFPHLTVLQNLL--LAPRKVLRIPMAEAKDRALTYLDKVGLGTKADN-YP 144 ++FQ + +L P L++ Q++L L K+ R +E K + L LDKVGL + N YP Sbjct: 400 QIIFQDPYASLNPKLSIGQSILEPLQVHKLYRND-SERKQKVLELLDKVGLKEEHFNRYP 458 Query: 145 DQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNVMKQLAEE-GMTMAVVT 203 + SGGQ+QRV IAR L ++P+ ++ DE SALD + +VLN++K L E G+T ++ Sbjct: 459 HEFSGGQRQRVVIARALALQPKFIICDESVSALDVSVQAQVLNLIKDLQSEFGLTYIFIS 518 Query: 204 HEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKS 239 H++ + +S+R+ N+G IEEEG P ++F PK+ Sbjct: 519 HDLAVVKHISDRILVMNKGKIEEEGFPEQIFYAPKA 554 Score = 102 bits (253), Expect = 2e-26 Identities = 70/246 (28%), Positives = 127/246 (51%), Gaps = 11/246 (4%) Query: 11 FDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRL--EVA 68 ++Q +K + + ++ ++ ++ V+ I+G SG GKS + RL ++ E+ Sbjct: 12 YNQEEKTW--FKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEID 69 Query: 69 GVDLSGAKIDQKHLRQLRV-RVGMVFQH--FNLFPHLTVLQNLLLAPRKVLRIPMAEAKD 125 D+S + +RQ+R ++ M+FQ +L P T + A ++ AEAK Sbjct: 70 FEDISLLNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKK 129 Query: 126 RALTYLDKVGLGTKA---DNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELV 182 + ++V L ++YP Q+SGGQKQRV IA L P++L+ DEPT+ALD + Sbjct: 130 HTIALFNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQ 189 Query: 183 GEVLNVMKQLAEE-GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDR 241 +L ++ +L +E M M ++H++ E+++ V +G I E+G +F NP+ Sbjct: 190 KTILQLLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIFENPQHPY 249 Query: 242 LRAFLS 247 + L+ Sbjct: 250 TKGLLA 255 Lambda K H 0.321 0.139 0.397 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: 362 Number of extensions: 21 Number of successful extensions: 8 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: 252 Length of database: 568 Length adjustment: 30 Effective length of query: 222 Effective length of database: 538 Effective search space: 119436 Effective search space used: 119436 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 (21.9 bits) S2: 50 (23.9 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