Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate 6938539 Sama_2642 polyamine ABC transporter, periplasmic polyamine-binding protein (RefSeq)
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__SB2B:6938539 Length = 366 Score = 457 bits (1177), Expect = e-133 Identities = 222/360 (61%), Positives = 277/360 (76%), Gaps = 1/360 (0%) Query: 8 TLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVLE 67 T LAL AG V G A + +V+ VYNWSDYIA DTLE F KETGI+V+YDV+D+NEVLE Sbjct: 8 TALALVTAG-VLGSAAVSAEEVVRVYNWSDYIAEDTLENFQKETGIRVIYDVFDTNEVLE 66 Query: 68 AKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNEH 127 AKLL+G+SGYD+VVPS FLAKQIKAG + KLDKSKL N K+LNK+LM L+ SDPGNEH Sbjct: 67 AKLLSGRSGYDLVVPSAHFLAKQIKAGAFMKLDKSKLTNEKHLNKNLMTQLQKSDPGNEH 126 Query: 128 AIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILPA 187 A+PY+WGT GIG+N KVK G++APVDSWDL+F P N +KL +CG++ LDSP EILP Sbjct: 127 AVPYLWGTTGIGFNVAKVKEVLGEDAPVDSWDLIFNPANAEKLAKCGIAVLDSPDEILPP 186 Query: 188 ALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIYQ 247 AL+YLG P++ +P + + A E+ LKIRPY+ YFHSS+YISDLANG IC AIG+SGD+ Q Sbjct: 187 ALNYLGLNPNSTDPADYEKAGEVLLKIRPYLKYFHSSRYISDLANGEICAAIGWSGDVLQ 246 Query: 248 AKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEITD 307 A++RAEEA N V Y IPKEGA +FDM+AIP DA N + AL F+N+LM+PE++A I++ Sbjct: 247 AQARAEEAGNGQQVDYRIPKEGAPLWFDMMAIPADAANADNALTFMNYLMRPEVIASISN 306 Query: 308 VVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSGK 367 V + N N + PL+ E + +P +YPSEE + KLY P KTQRAMTR WTKIKSG+ Sbjct: 307 YVAYANANDGSNPLLDEEVAKNPAVYPSEETLAKLYLGEVRPMKTQRAMTRIWTKIKSGQ 366 Lambda K H 0.315 0.133 0.390 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: 473 Number of extensions: 12 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: 367 Length of database: 366 Length adjustment: 30 Effective length of query: 337 Effective length of database: 336 Effective search space: 113232 Effective search space used: 113232 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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