Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate SMc00771 SMc00771 putrescine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Smeli:SMc00771 Length = 381 Score = 399 bits (1026), Expect = e-116 Identities = 203/362 (56%), Positives = 272/362 (75%), Gaps = 2/362 (0%) Query: 15 ALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAG 74 A P + ++N+TK + AVDD+SL IY E FALLGASGCGKSTLLRMLAGFEQP++G Sbjct: 19 ASKPFISVKNVTKKFGDFTAVDDLSLNIYTREFFALLGASGCGKSTLLRMLAGFEQPTSG 78 Query: 75 QIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEML 134 +I+LDG L+ +PPY RP+NMMFQSYALFPHMTVE N+AFGLKQD +PKA+IA RV +ML Sbjct: 79 EIILDGQSLAGIPPYRRPVNMMFQSYALFPHMTVENNVAFGLKQDGMPKADIAERVAQML 138 Query: 135 GLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVD 194 LV +++FAKRKPHQLSGGQRQRVALARSLAKRPK+LLLDEP+GALDKKLR+ Q E++D Sbjct: 139 KLVKLEKFAKRKPHQLSGGQRQRVALARSLAKRPKVLLLDEPLGALDKKLREETQFELMD 198 Query: 195 ILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVN 254 + + +G+T V+VTHDQEEAMTMA RIA+M+ GK VQ+ P EIYE P +R+ A+FIG VN Sbjct: 199 LQQELGLTFVVVTHDQEEAMTMADRIAVMSHGKVVQVATPAEIYEAPNSRFVADFIGDVN 258 Query: 255 VFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANG-C 313 +F+G + ++ + +++ G + P+++ + + VA+RPEKI + +PPA+ Sbjct: 259 IFDGKVTSAEDGYIRVETTGGI-PVRMASPEKPGNGAKAAVAIRPEKIRIGRQPPAHAPV 317 Query: 314 NFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCV 373 N A GE+ I YLGD++V+H+RLK G+++ A NA R + + +V + + D+ V Sbjct: 318 NAAEGEIWDIGYLGDMTVFHIRLKDGKVVKASSLNAVRAVEDPLGYDQQVWISFGDDAGV 377 Query: 374 VL 375 VL Sbjct: 378 VL 379 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: 432 Number of extensions: 17 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: 381 Length adjustment: 30 Effective length of query: 347 Effective length of database: 351 Effective search space: 121797 Effective search space used: 121797 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: 50 (23.9 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