Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate 3607646 Dshi_1055 ABC transporter related (RefSeq)
Query= TCDB::P31134 (377 letters) >FitnessBrowser__Dino:3607646 Length = 366 Score = 254 bits (649), Expect = 3e-72 Identities = 148/364 (40%), Positives = 217/364 (59%), Gaps = 10/364 (2%) Query: 13 RKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPS 72 R+ P +E++ L+K Y A+ V LTI GE F LLG SG GK+TLLR + GF +P+ Sbjct: 2 RQTTPPAVEVKGLSKHYGPVKALRQVDLTIAAGEYFVLLGPSGGGKTTLLRTIGGFHRPT 61 Query: 73 AGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNE 132 GQ++L G D+S +PP RP M+FQ+YALFPHMTV QN+++GLK + KA + Sbjct: 62 EGQVLLHGRDMSHLPPDKRPTTMVFQAYALFPHMTVLQNVSYGLKVAGMDKATAQEKAAA 121 Query: 133 MLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEV 192 M+ +V + FA+RKPH+LSGGQ+QRV LAR+L +LLLDEP+ ALD +LR M LE+ Sbjct: 122 MMDVVGLAGFAERKPHELSGGQQQRVQLARALVLDRDILLLDEPLAALDAQLRKDMCLEL 181 Query: 193 VDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGS 252 + E+VG+T + VTH+QEEAMT+A RIA++ G+ V+ G +IY P +++A F+G Sbjct: 182 KHLQEKVGITFIHVTHNQEEAMTVADRIALVADGQLVEQGAARDIYRAPIKKFTAGFVGE 241 Query: 253 VNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIML----CEEP 308 N+ G + + +++ G + V V +++R E + L Sbjct: 242 NNLLSGTVSQVNGVSCMVEVAGAQLSVP-KRGQEVTQGQAVDLSIRSELVQLSRVDASND 300 Query: 309 PANGCNFAVGEVIHIAYLGDLSVYHVRLKSG-QMISAQLQNAHRHRKGLPTWGDEVRLCW 367 P +G + +G YLG + + VRL +G +M S + +A LPT GD VRL W Sbjct: 301 PGDG-HSILGSYDEAVYLGLTTSHLVRLPNGVEMTSRTISDA---LGDLPTPGDPVRLSW 356 Query: 368 EVDS 371 + D+ Sbjct: 357 QPDA 360 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: 358 Number of extensions: 16 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: 377 Length of database: 366 Length adjustment: 30 Effective length of query: 347 Effective length of database: 336 Effective search space: 116592 Effective search space used: 116592 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