Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 168 bits (425), Expect = 2e-46 Identities = 95/292 (32%), Positives = 168/292 (57%), Gaps = 11/292 (3%) Query: 24 SLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNI 83 ++ +V N G +ALLG SG GK+TLL +++G +P+ GRI DG+D+T++ R I Sbjct: 35 AVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLDGQDITDMPPYERPI 94 Query: 84 AQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTAD 143 +FQ ++ MTV N+AF L+ + +A++++RV+++L+++ + +A+RK L+ Sbjct: 95 NMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHMEPYAKRKPNQLSGG 154 Query: 144 QKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTE 203 Q+Q+++L R L + +L DEP+ +D ++ ++ ++ + + G T V VTHDQ E Sbjct: 155 QRQRVALARSLAKRP-KLLLLDEPMGALDKKLRTQMQLEVVDILEAVGVTCVMVTHDQEE 213 Query: 204 ALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGM---NFMPARIEGSTVKV 260 A+T AE++ +M DG I Q G+P +++E P++ V FIGS + + + ++ + V Sbjct: 214 AMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGSVNLFEGDIVEDEVDHVVINV 273 Query: 261 GD--ETLTLEYAPKTS-GTAKTELGIRPEFIRLGRE----GMPITISKVEDI 305 + + + Y TS T + + IRPE + RE KVEDI Sbjct: 274 ANIPQPFYVGYGVSTSVDTTQVWVAIRPEKTHISREQPEDARNWCAGKVEDI 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: 301 Number of extensions: 13 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: 378 Length adjustment: 30 Effective length of query: 326 Effective length of database: 348 Effective search space: 113448 Effective search space used: 113448 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