Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_086509877.1 BZY95_RS10495 polyamine ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >NCBI__GCF_002151265.1:WP_086509877.1 Length = 358 Score = 437 bits (1125), Expect = e-127 Identities = 230/357 (64%), Positives = 270/357 (75%), Gaps = 2/357 (0%) Query: 20 LEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIMLD 79 +EIR ++K +DG AVDDVSL+I +GEIFALLG SG GKSTLLRMLAGFE+PS GQI+LD Sbjct: 1 MEIRRVSKRFDGVLAVDDVSLSIRRGEIFALLGGSGSGKSTLLRMLAGFEKPSEGQIVLD 60 Query: 80 GVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHM 139 G D++ +PPY RPINMMFQSYALFPHMTV QNIAFGLKQD+LP+ EI RV EML LVHM Sbjct: 61 GEDITTMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDRLPRREIEERVAEMLKLVHM 120 Query: 140 QEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERV 199 + +A+RKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLR MQLEVV ILERV Sbjct: 121 EAYARRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTEMQLEVVQILERV 180 Query: 200 GVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEGV 259 GVTC+MVTHDQEEAMTMA R+AIM+ G Q+G P ++YE P R AEF+GSVN+FEG Sbjct: 181 GVTCIMVTHDQEEAMTMADRVAIMSDGWIAQVGTPMDVYESPANRMVAEFVGSVNLFEGD 240 Query: 260 LKERQEDGLVLDSPGLVHPLKVDADASV-VDNVPVHVALRPEKIMLCEEPPANGCNFAVG 318 + + D V++SP L P+++ S D V VALRPEK L E P N+ G Sbjct: 241 IVVDEVDHCVIESPALSRPIRIGHGVSTQADERRVWVALRPEKTGLTRERPQGDSNWEAG 300 Query: 319 EVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDSCVVL 375 V IAYLG LSVY VRL+SGQ++ A + N R R P W + V + W+ S V+L Sbjct: 301 VVEDIAYLGGLSVYFVRLESGQLVKASMANTER-RGDRPRWDEPVFVHWDEHSAVIL 356 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: 446 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: 358 Length adjustment: 30 Effective length of query: 347 Effective length of database: 328 Effective search space: 113816 Effective search space used: 113816 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 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