Align spermidine/putrescine ABC transporter, permease protein PotB (characterized)
to candidate WP_010960191.1 MCA_RS04290 spermidine/putrescine ABC transporter permease PotB
Query= CharProtDB::CH_088337 (275 letters) >NCBI__GCF_000008325.1:WP_010960191.1 Length = 284 Score = 296 bits (758), Expect = 3e-85 Identities = 140/262 (53%), Positives = 193/262 (73%) Query: 5 IVGWLVLFVFLPNLMIIGTSFLTRDDASFVKMVFTLDNYTRLLDPLYFEVLLHSLNMALI 64 + GWL+ FV P L+++G S L+R A F TLDNY RL DP+Y V S A I Sbjct: 16 LAGWLLSFVLAPTLLVVGLSLLSRSPAGFAGGPVTLDNYRRLADPIYLHVFAESFATAFI 75 Query: 65 ATLACLVLGYPFAWFLAKLPHKVRPLLLFLLIVPFWTNSLIRIYGLKIFLSTKGYLNEFL 124 ATL CL+LGYPFA+ LA+ +RPLLL L+IVPFWT+SL+RIY ++ L+ KG LN L Sbjct: 76 ATLLCLLLGYPFAYGLARARPGLRPLLLILVIVPFWTSSLVRIYAIRGLLAAKGALNHLL 135 Query: 125 LWLGVIDTPIRIMFTPSAVIIGLVYILLPFMVMPLYSSIEKLDKPLLEAARDLGASKLQT 184 L G+ D P+R+++T +A I+GLV++LLPFM++PLY+S+EKLD LLEAARDLGA + Sbjct: 136 LAAGLSDQPVRLLYTQTAEIVGLVHVLLPFMILPLYASLEKLDPRLLEAARDLGAGPFRR 195 Query: 185 FIRIIIPLTMPGIIAGCLLVMLPAMGLFYVSDLMGGAKNLLIGNVIKVQFLNIRDWPFGA 244 F +++PLT+PG++AGCLLV LPA+GLFYV D++GG+++LL+GN++K QFL +DWPFGA Sbjct: 196 FRHVVLPLTLPGVVAGCLLVFLPALGLFYVGDVLGGSRHLLVGNLLKDQFLEAQDWPFGA 255 Query: 245 ATSITLTIVMGLMLLVYWRASR 266 A S+ L ++ L +Y A++ Sbjct: 256 AASLVLIGLLLAFLALYAYAAK 277 Lambda K H 0.333 0.148 0.456 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: 309 Number of extensions: 15 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: 275 Length of database: 284 Length adjustment: 26 Effective length of query: 249 Effective length of database: 258 Effective search space: 64242 Effective search space used: 64242 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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