Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SMc02518 SMc02518 ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Smeli:SMc02518 Length = 356 Score = 586 bits (1511), Expect = e-172 Identities = 283/356 (79%), Positives = 317/356 (89%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MARI L+HIRHAYGA PKS+ DY+L+EV HEWNDGGAYALLGPSGCGKTTLLNIISGL+ Sbjct: 1 MARINLEHIRHAYGARPKSESDYALREVHHEWNDGGAYALLGPSGCGKTTLLNIISGLIN 60 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 PS GRILFDG DVT+L+TQ RNIAQVFQFPVIYDTMTVYDNLAFPLRNR V E +VDRRV Sbjct: 61 PSEGRILFDGTDVTHLTTQQRNIAQVFQFPVIYDTMTVYDNLAFPLRNRHVPETEVDRRV 120 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 ++ILEM L SWA++ A+GLTADQKQKISLGRGLVR+DV+AILFDEPLTVIDP MKWVLR Sbjct: 121 KEILEMTGLGSWAKKTARGLTADQKQKISLGRGLVRSDVSAILFDEPLTVIDPEMKWVLR 180 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 SQ+KRLHKQFGFTMVYVTHDQTEALTFA+KVVVMYDGQIVQIGTPAELFERP HTFVGYF Sbjct: 181 SQIKRLHKQFGFTMVYVTHDQTEALTFADKVVVMYDGQIVQIGTPAELFERPRHTFVGYF 240 Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREGMPITIS 300 IGSPGMN +PA I G+T VGD+ + L + P+ A+ ELGIRPEFI LGREGMP+ ++ Sbjct: 241 IGSPGMNVLPAEIAGNTAAVGDQRIALNFQPQIKAGARIELGIRPEFISLGREGMPVAVT 300 Query: 301 KVEDIGRQKIVRARFADQPIAIVVPEDADIPADARVTFDPSAISIYADSWRVGREA 356 KVEDIGR K+VRARFAD+PI+I+V ED +IPA+ RVTFDP AI+IYADSWRVG EA Sbjct: 301 KVEDIGRHKVVRARFADRPISIIVDEDGEIPAEPRVTFDPKAINIYADSWRVGGEA 356 Lambda K H 0.321 0.137 0.405 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: 518 Number of extensions: 12 Number of successful extensions: 1 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: 356 Length of database: 356 Length adjustment: 29 Effective length of query: 327 Effective length of database: 327 Effective search space: 106929 Effective search space used: 106929 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 (21.8 bits) S2: 49 (23.5 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