Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 174 bits (440), Expect = 4e-48 Identities = 92/239 (38%), Positives = 144/239 (60%), Gaps = 7/239 (2%) Query: 4 ITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSH 63 IT +++ +G K ++ V N+G +ALLGPSGCGKTTLL +++G P+ Sbjct: 15 ITFENVTKRFG------KLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTE 68 Query: 64 GRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDI 123 GRIL DG+D++N+ R + VFQ ++ MTV DN+A+ L+ V +A+ + RV + Sbjct: 69 GRILIDGQDISNVPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEA 128 Query: 124 LEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQL 183 LE++ L RK L+ Q+Q+++L R LV+ +L DEPL+ +D ++ +R++L Sbjct: 129 LELVQLGGLGGRKPDQLSGGQRQRVALARALVKRP-RVLLLDEPLSALDAKLREQMRTEL 187 Query: 184 KRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIG 242 L ++ G T + VTHDQ EAL A + VM G + Q+ TP++L+E P+ FV FIG Sbjct: 188 CTLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIG 246 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: 312 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: 381 Length adjustment: 30 Effective length of query: 326 Effective length of database: 351 Effective search space: 114426 Effective search space used: 114426 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