Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_011612352.1 TERY_RS13510 polyamine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_000014265.1:WP_011612352.1 Length = 381 Score = 264 bits (675), Expect = 3e-75 Identities = 152/358 (42%), Positives = 225/358 (62%), Gaps = 9/358 (2%) Query: 24 NLTKSYDGQH-----AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78 N+ K + Q+ AV++++L I K E F++LG SGCGK+T LRM+AGFE P++G+I + Sbjct: 10 NIGKIFSSQNKKQFIAVNNINLQIKKSEFFSILGPSGCGKTTTLRMIAGFEIPTSGEIYI 69 Query: 79 DGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVH 138 + PP+ RP+N +FQ+YALFPH+TV +NIAFGL+ + LP+ EI RV + L V Sbjct: 70 QDKLMGNSPPFHRPVNTVFQNYALFPHLTVAENIAFGLEMENLPRPEINRRVADSLAQVK 129 Query: 139 MQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILER 198 + + K P +LSGGQ+QRVALAR+L K+P +LL DEP+GALD KLR MQLE+ + +R Sbjct: 130 LIDMQKFYPRKLSGGQQQRVALARALIKQPAVLLFDEPLGALDLKLRQEMQLELKLMQQR 189 Query: 199 VGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEG 258 +G+T + VTHDQEEA+TM+ RIA+M+ G+ +Q+G P EIYE P +R+ AEFIG N G Sbjct: 190 LGMTFIYVTHDQEEALTMSDRIAVMHHGEVLQVGTPVEIYEQPKSRFVAEFIGESNFLTG 249 Query: 259 VLKERQED-GLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPANGCNFAV 317 + QED +VL L L + + + + + +RPEKI + NF+ Sbjct: 250 GIIAHQEDKSMVLIDEDL--RLLIPSVNHLPIGTVITLVVRPEKIEIFPPNFTAKYNFS- 306 Query: 318 GEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVVL 375 G + ++ YLG + Y V L I + QN + + G++V++ V++ +L Sbjct: 307 GRIENLVYLGTDTRYVVGLNDKIKIVIRRQNINLFYLNQYSVGEKVKVHIPVENISIL 364 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: 354 Number of extensions: 9 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: 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 24 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