Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate Pf1N1B4_4895 Putrescine ABC transporter, periplasmic putrescine-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4895 Length = 361 Score = 434 bits (1116), Expect = e-126 Identities = 207/360 (57%), Positives = 270/360 (75%), Gaps = 3/360 (0%) Query: 7 KTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEVL 66 KTL LA VA +QAA+ + +YNWSDYIAPDT + F KETGI YDV+DSNE L Sbjct: 4 KTLTLAPLA-LVATFSQAAET--VKIYNWSDYIAPDTTKNFQKETGIAFSYDVFDSNETL 60 Query: 67 EAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGNE 126 + KL+ G SGYDVV PSN F+A+QI+ G +KLDKS+LPNWKNLN L+ TL+ +DPGNE Sbjct: 61 DGKLMTGTSGYDVVFPSNHFMARQIEGGALKKLDKSQLPNWKNLNPVLLQTLQANDPGNE 120 Query: 127 HAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEILP 186 H PY+WG+ GIGYN KVKA GDNAPVDSWDL+FKPEN+ KL++CGV+ LD+ E+LP Sbjct: 121 HGFPYLWGSTGIGYNVAKVKAVLGDNAPVDSWDLIFKPENMAKLQKCGVAILDNGPELLP 180 Query: 187 AALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDIY 246 AAL+YLG + NP++ K AE L +K+RPYV+YFHSSKY SDLANG+ICVA+G+SGDI Sbjct: 181 AALNYLGLPHHSKNPEDYKKAEALLMKVRPYVSYFHSSKYTSDLANGDICVAVGFSGDII 240 Query: 247 QAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEIT 306 QA++RA+EA+N V + Y+IPKEGA +FDMVA+P DA + + AF+N+L++P++MA I+ Sbjct: 241 QAENRAKEARNGVDIGYSIPKEGAAIWFDMVAMPADAPDEKAGYAFMNYLLRPDVMAGIS 300 Query: 307 DVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKSG 366 + V + NGN A L+ AI++D +YPS E+M KL+ +P R TR W KI++G Sbjct: 301 NYVHYANGNEQADNLIDPAIKSDTKVYPSPEMMGKLFALEAMPLNIDRVRTRVWNKIRTG 360 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: 493 Number of extensions: 19 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: 361 Length adjustment: 29 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 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