Align putrescine transport system permease protein PotH (characterized)
to candidate CCNA_03238 CCNA_03238 ABC-type spermidine/putrescine transport system, permease component II
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__Caulo:CCNA_03238 Length = 306 Score = 205 bits (522), Expect = 1e-57 Identities = 109/282 (38%), Positives = 168/282 (59%), Gaps = 28/282 (9%) Query: 36 PYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLGNFLQLTDDPLY 95 P +WL+L FL P IV+ S +++I+ N+ + + PLY Sbjct: 23 PLVWLVLFFLAPMAIVWAYSFGHNVGLT------------EIAISGTFHNYARAIE-PLY 69 Query: 96 FDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSFLIRVYAWM 155 +L+S+ VA ++T CL+IG+P+A A+ + + LLLL++LP WT+ LIR YA + Sbjct: 70 LKIFLKSVWVAGLTTGLCLVIGFPVALAITFASDKAKAWLLLLIMLPFWTNLLIRTYALI 129 Query: 156 GILKNNGVLNNFLLWL-----GVID----------QPLTILHTNLAVYIGIVYAYVPFMV 200 +L+ G +N L W G+ QPL +LH N AV +G+VY ++PFMV Sbjct: 130 AVLRTEGYVNQGLEWFWKGGSGLATLIGLQPLGDFQPLELLHNNFAVILGLVYVHLPFMV 189 Query: 201 LPIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPE 260 LP+Y+AL R+D SL+EA+LDLGA L+T F V+VPL GI +G ++ FIPA+G ++ P+ Sbjct: 190 LPLYSALDRLDKSLLEASLDLGAGHLRTLFKVVVPLAIPGIASGVLITFIPALGAYLTPD 249 Query: 261 LLGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPI 302 LLGGPDS MI ++ ++F DWP +A++ +++ L + I Sbjct: 250 LLGGPDSQMIANIIERQFKRANDWPFGAALSFLLMYLTFIAI 291 Lambda K H 0.328 0.144 0.457 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: 299 Number of extensions: 17 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: 317 Length of database: 306 Length adjustment: 27 Effective length of query: 290 Effective length of database: 279 Effective search space: 80910 Effective search space used: 80910 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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