Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= TCDB::P31134 (377 letters) >MicrobesOnline__882:209225 Length = 354 Score = 173 bits (438), Expect = 7e-48 Identities = 111/291 (38%), Positives = 154/291 (52%), Gaps = 24/291 (8%) Query: 19 LLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78 +L + L ++ G+ + DV+LT GE+ L+G SG GK+TLLR +AG + P G I + Sbjct: 2 VLAVEGLGRTLAGREVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRV 61 Query: 79 DGVDLSQVPP--YLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEML-- 134 PP + + ++FQ Y LFPH++V +N+AFG + + A + RV+ ML Sbjct: 62 -------TPPQGHGGGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRA 114 Query: 135 ------GLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRM 188 L HM A R P QLS GQRQRVALAR+L P +LLLDEP LD+ LR M Sbjct: 115 FRLDTDDLAHM---ASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEM 171 Query: 189 QLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAE 248 V D++ R GV V VTHD EEA + R+ +M G Q+ P ++Y HP +A Sbjct: 172 AAFVRDVVRRFGVATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATAR 231 Query: 249 FIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRP 299 F+G V VL E L +D+P D + P +A+RP Sbjct: 232 FLGPVT----VLDETTRRTLGIDTPPAAATACADTMQGLRLYRPEALAVRP 278 Lambda K H 0.321 0.137 0.400 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: 351 Number of extensions: 15 Number of successful extensions: 3 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: 377 Length of database: 354 Length adjustment: 30 Effective length of query: 347 Effective length of database: 324 Effective search space: 112428 Effective search space used: 112428 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