Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate SMc01631 SMc01631 ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Smeli:SMc01631 Length = 359 Score = 287 bits (734), Expect = 4e-82 Identities = 150/325 (46%), Positives = 209/325 (64%), Gaps = 11/325 (3%) Query: 15 ALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAG 74 A T +E R++ K Y AV D++LT+ KG ALLG SGCGK+T LRM+ GFEQPS G Sbjct: 4 ASTNDIEFRSVAKRYGSVTAVSDINLTVPKGAFVALLGPSGCGKTTCLRMIGGFEQPSEG 63 Query: 75 QIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDK--LPKAEIASRVNE 132 + + G ++ VP Y RP+NM+FQ YALFPH+ VEQN+A+GLKQ + +P AEI R E Sbjct: 64 MVYIGGQPMNGVPAYRRPVNMVFQQYALFPHLDVEQNVAYGLKQTRPRIPAAEITRRAQE 123 Query: 133 MLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEV 192 L +V + F KR+ H++SGGQ+QRVALAR++ +PK+LLLDEP+ ALDKKLR MQ+E+ Sbjct: 124 ALEMVRLGGFGKRRIHEMSGGQQQRVALARAIVNKPKVLLLDEPLAALDKKLRTAMQIEL 183 Query: 193 VDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGS 252 + +G+T V+VTHDQEEA++M+ + +M+ G+ VQIG P+EIY+ P + + A+F+G Sbjct: 184 QSLQRELGITFVLVTHDQEEALSMSDFVCVMSTGRIVQIGPPQEIYDRPASLFVADFVGK 243 Query: 253 VNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANG 312 N G ++ L+ + GL P + + A PV VALRPE I L + G Sbjct: 244 TNRIAGTIEPGAGAVLLANGVGLAKPARANGTAG-----PVMVALRPEAISLVRD----G 294 Query: 313 CNFAVGEVIHIAYLGDLSVYHVRLK 337 G V H +LG Y V ++ Sbjct: 295 SAALRGTVTHRIFLGSSVEYSVEVE 319 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: 342 Number of extensions: 12 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: 359 Length adjustment: 30 Effective length of query: 347 Effective length of database: 329 Effective search space: 114163 Effective search space used: 114163 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