Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate PP_1722 PP_1722 ABC transporter, ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Putida:PP_1722 Length = 329 Score = 177 bits (448), Expect = 5e-49 Identities = 117/349 (33%), Positives = 181/349 (51%), Gaps = 30/349 (8%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 M+ +++ ++ +Y +P ++ +D G LLGPSGCGK+TLL I+GL Sbjct: 1 MSFVSVQKLQKSYAGSPVFER------IDCHIERGEFVTLLGPSGCGKSTLLRCIAGLTS 54 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 G+IL DG D+ LS Q R I VFQ ++ MTV N+AF LR + V + RV Sbjct: 55 VDSGQILLDGHDIVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVKADESQLRV 114 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 R++LE+++L +A R L+ Q Q+++L R LV +L DEPL+ +D ++ LR Sbjct: 115 REVLELVELGKFAGRYPHQLSGGQCQRVALARSLVTRP-RLLLLDEPLSALDARIRKHLR 173 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 Q++ + ++ G T ++VTHDQ EALT ++++ +M G+IVQ G L+ P F F Sbjct: 174 EQIRAIQRELGLTTIFVTHDQEEALTMSDRIFLMNQGRIVQSGDAETLYTAPVDLFAAGF 233 Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREG-MPITI 299 IG+ N + A D L P S L IRPE I LG G + + Sbjct: 234 IGN--YNLLDA----------DSASRLLQRPVAS-----RLAIRPESITLGEHGELDAEV 276 Query: 300 SKVEDIGR--QKIVRARFADQPIAIVVPEDADIPADAR---VTFDPSAI 343 +G + VR R + + ++ AD+ AD + V+ DP+A+ Sbjct: 277 RSHSLLGNVIRYRVRVREVELVVDVLNRSPADLHADGKRVSVSIDPTAL 325 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: 240 Number of extensions: 8 Number of successful extensions: 2 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: 329 Length adjustment: 29 Effective length of query: 327 Effective length of database: 300 Effective search space: 98100 Effective search space used: 98100 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