Align spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein PotD (characterized)
to candidate GFF4125 HP15_4065 spermidine/putrescine ABC transporter periplasmic substrate-binding protein
Query= CharProtDB::CH_088339 (348 letters) >FitnessBrowser__Marino:GFF4125 Length = 346 Score = 371 bits (953), Expect = e-107 Identities = 172/345 (49%), Positives = 248/345 (71%), Gaps = 2/345 (0%) Query: 6 RHLLAAGALALGMSAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETM 65 + L AG LA+G++ +++ L YNW+EY+P +L++FT+ETGI+V+Y+TY+SNE M Sbjct: 2 KKLALAGLLAVGLTGCSSEEPQVLNLYNWSEYMPQEVLDRFTEETGIQVVYTTYDSNEAM 61 Query: 66 YAKLKTYKDGA-YDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNND 124 YA+LK D A YDL VPSTYYV KMR+E ++ ID+SK+ F NLDP+++N DP N Sbjct: 62 YARLKLLDDSAAYDLAVPSTYYVSKMRQEDLLLPIDRSKIEGFDNLDPELVNLDIDPENQ 121 Query: 125 YSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSG 184 +S+PY+WG T + V+ ++ + VT+W DLW+ + G ++LT+D REVF + LR LGYSG Sbjct: 122 FSVPYLWGTTGLAVDTADIEGEPVTAWEDLWEDRFDGRVMLTNDMREVFHVGLRVLGYSG 181 Query: 185 NTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPID 244 N+T+P EIEAAY +L +LMP+V FNSD P PY+EGE ++GMIWNG A + + ++ Sbjct: 182 NSTNPDEIEAAYEKLAELMPSVRTFNSDAPRMPYLEGEADVGMIWNGEAVMGKDTMESLE 241 Query: 245 VVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLL 304 V+P+EG I W+DS IP NAKN E A + I+F+L+P+++ ++E IGY TPNLAAR LL Sbjct: 242 YVYPEEGIIAWLDSFVIPKNAKNPEAAHQFISFVLQPEISALISEEIGYATPNLAARDLL 301 Query: 305 SPEVANDKTLYPDAETIKNGEWQNDVG-AASSIYEEYYQKLKAGR 348 EVAN++ YP+A + N E+Q D+G A +Y +Y++ LK+GR Sbjct: 302 PDEVANNRASYPNATDMINAEFQTDIGDDALQVYAKYWEMLKSGR 346 Lambda K H 0.314 0.132 0.397 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: 461 Number of extensions: 16 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: 348 Length of database: 346 Length adjustment: 29 Effective length of query: 319 Effective length of database: 317 Effective search space: 101123 Effective search space used: 101123 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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