Align Putrescine-binding periplasmic protein (characterized)
to candidate H281DRAFT_05180 H281DRAFT_05180 putrescine transport system substrate-binding protein
Query= SwissProt::P31133 (370 letters) >FitnessBrowser__Burk376:H281DRAFT_05180 Length = 366 Score = 383 bits (983), Expect = e-111 Identities = 182/366 (49%), Positives = 258/366 (70%), Gaps = 2/366 (0%) Query: 6 KKWLSGLVAGALMAVSVG-TLAAEQKTLHIYNWSDYIAPDTVANFEKETGIKVVYDVFDS 64 K+ + G VA ++ + T AA+ L++YNWSDYIA DT+ NF K+TG++V YD +DS Sbjct: 2 KRRVVGQVAALVLCAAPWLTAAAKDTQLNVYNWSDYIAKDTIPNFTKQTGVQVKYDNYDS 61 Query: 65 NEVLEGKLMAGSTGFDLVVPSASFLERQLTAGVFQPLDKSKLPEWKNLDPELLKLVAKHD 124 ++ L+ KL+ G++G+D+VVP++++ +Q+ AG+F PLDKSKLP K LDP L+ LVA D Sbjct: 62 DDTLQAKLLTGNSGYDIVVPTSNYAGKQIAAGIFSPLDKSKLPNLKYLDPSLMSLVAGAD 121 Query: 125 PDNKFAMPYMWATTGIGYNVDKVKAVLGENAPVDSWDLILKPENLEKLKSCGVSFLDAPE 184 PDNKF +P+ + TTG+GYNV K + +LG+N P+D+WD++ KPEN+ KLK+CGVS LDAP+ Sbjct: 122 PDNKFTVPWAYGTTGLGYNVTKAQQILGKNVPLDNWDILFKPENISKLKACGVSVLDAPD 181 Query: 185 EVFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHSSQYINDLANGDICVAIGW 244 ++FA L+Y+GKDP ST DY A +L K+RP I F+SS YINDL GD+C A GW Sbjct: 182 QMFAAALHYIGKDPMSTNPADYRA-ALAMLKKIRPYITQFNSSGYINDLVGGDVCFAYGW 240 Query: 245 AGDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLLRPDV 304 +GDV A +RA EAK + + IPK GA +FDV A+P DAK+K+ A +++NY+ P V Sbjct: 241 SGDVVIAKHRAIEAKKAYKIEYYIPKGGAPVWFDVMAIPKDAKHKEAALEWINYIETPQV 300 Query: 305 VAHISDHVFYANANKAATPLVSAEVRENPGIYPPADVRAKLFTLKVQDPKIDRVRTRAWT 364 A I++ V+Y +AN A V +V +P +YPP DV LF LK P++ R++TR WT Sbjct: 301 HAAITNAVYYPSANLEARKYVDKDVANDPAVYPPPDVIKTLFLLKPLPPEVQRLQTRLWT 360 Query: 365 KVKSGK 370 + KSG+ Sbjct: 361 EFKSGR 366 Lambda K H 0.317 0.133 0.400 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: 16 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: 370 Length of database: 366 Length adjustment: 30 Effective length of query: 340 Effective length of database: 336 Effective search space: 114240 Effective search space used: 114240 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: 41 (21.6 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