Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 195 bits (496), Expect = 1e-54 Identities = 111/301 (36%), Positives = 178/301 (59%), Gaps = 11/301 (3%) Query: 31 GQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLDGVDLSQVPPYL 90 G+ + D++L + +GE F +LG +G GK+ +L +AG +P G I +L+ + P Sbjct: 12 GEFQLLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQ 71 Query: 91 RPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHMQEFAKRKPHQL 150 R + ++Q YALFPH+TV++NI FG + KLPK I S+++E++ ++ + R P L Sbjct: 72 RKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTL 131 Query: 151 SGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCVMVTHDQ 210 SGG++QR ALAR+L P++LLLDEP+ ALD + ++ Q E+ I + + T + VTHD Sbjct: 132 SGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDF 191 Query: 211 EEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEGVLKERQEDGLVL 270 EAM +A +I +M++G+ +Q+G P+EI+ P + A F+G N+FEG + D V Sbjct: 192 NEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVGIENIFEG----QVNDDKVS 247 Query: 271 DSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNFAV-GEVIHIAYLGDL 329 +P VD + V VA+ PE I L +EP ++ G+V++I+ G L Sbjct: 248 LAP------DVDIFVNTGKQGKVKVAVPPEDIALSKEPFDLCYHYQFNGKVLNISNQGAL 301 Query: 330 S 330 S Sbjct: 302 S 302 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: 303 Number of extensions: 16 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: 377 Length of database: 344 Length adjustment: 29 Effective length of query: 348 Effective length of database: 315 Effective search space: 109620 Effective search space used: 109620 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 Apr 09 2024. 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