Align Spermidine/putrescine ABC transporter, permease protein, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate 350817 BT1289 putrescine transport system permease protein potI (NCBI ptt file)
Query= TCDB::Q97Q44 (257 letters) >FitnessBrowser__Btheta:350817 Length = 265 Score = 178 bits (451), Expect = 1e-49 Identities = 98/261 (37%), Positives = 162/261 (62%), Gaps = 7/261 (2%) Query: 2 KKFANLYLGLVFLVLYLPIFYLIGYAFNAGDDMNSFTGFSWTHFETMFGDGR---LMLIL 58 K FA YL ++ L+LY PI ++ Y+F + ++TGFS + ++F G LM L Sbjct: 4 KIFAQTYLWVLLLLLYSPIVIIVIYSFTEAKVLGNWTGFSTKLYSSLFNTGAHHSLMNAL 63 Query: 59 AQTFFLAFLSALIATIIGTFGAIYIYQSRKKYQEAFLSLNNILMVAPDVMIGASFLILFT 118 T +A L+A +T++G+ AI I+ + + ++A +N+I ++ D++ G S +LF Sbjct: 64 INTITIALLAATASTLLGSIAAIGIFNLKARSRKAIGFVNSIPILNGDIITGISLFLLFV 123 Query: 119 QLKFSLGFLTVLSSHVAFSIPIVVLMVLPRLKEMNGDMIHAAYDLGASQFQMFKEIMLPY 178 L + G+ TV+ +H+ F P VVL VLPRLK+MN ++ AA DLGA+ Q +++++P Sbjct: 124 SLGITQGYTTVVLAHITFCTPYVVLSVLPRLKQMNPNIYEAALDLGATPMQALRKVIIPE 183 Query: 179 LTPSIITGYFMAFTYSLDDFAVTFFVTGN-GFSTLSVEIYSRARK-GISLEINALSALVF 236 + P +I+G+ +A T S+DDFAVT F GN G TLS IY+ ARK G++ E+ LSA++F Sbjct: 184 IRPGMISGFMLALTLSIDDFAVTVFTIGNQGLETLSTYIYADARKGGLTPELRPLSAIIF 243 Query: 237 --LFSIILVVGYYFISREKEE 255 + ++++V+ Y +K+E Sbjct: 244 VVVLALLIVINYRAGKTKKKE 264 Lambda K H 0.332 0.145 0.418 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: 188 Number of extensions: 13 Number of successful extensions: 4 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: 257 Length of database: 265 Length adjustment: 25 Effective length of query: 232 Effective length of database: 240 Effective search space: 55680 Effective search space used: 55680 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 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