Align Putrescine-binding periplasmic protein SpuD (characterized)
to candidate BPHYT_RS23150 BPHYT_RS23150 ABC transporter substrate-binding protein
Query= SwissProt::Q02UB7 (367 letters) >FitnessBrowser__BFirm:BPHYT_RS23150 Length = 373 Score = 359 bits (922), Expect = e-104 Identities = 176/361 (48%), Positives = 243/361 (67%) Query: 6 GKTLLALTLAGSVAGMAQAADNKVLHVYNWSDYIAPDTLEKFTKETGIKVVYDVYDSNEV 65 G LLA T +++ A + L+VYNWSDYIA DT+ F K+ GIKV YD YDS++ Sbjct: 12 GAALLAFTGFAALSVTPALAADTELNVYNWSDYIAKDTISNFEKQDGIKVKYDNYDSDDT 71 Query: 66 LEAKLLAGKSGYDVVVPSNSFLAKQIKAGVYQKLDKSKLPNWKNLNKDLMHTLEVSDPGN 125 L+AKLLAG SGYD+VVP+++++AKQI+AGVYQKLDKSKLPN NL+ LM + +DPGN Sbjct: 72 LQAKLLAGSSGYDIVVPTSNYMAKQIQAGVYQKLDKSKLPNLANLDPVLMKMIADADPGN 131 Query: 126 EHAIPYMWGTIGIGYNPDKVKAAFGDNAPVDSWDLVFKPENIQKLKQCGVSFLDSPTEIL 185 ++ +P+ +GT GIGYN V+ A G NAPVDSW LVF P N+ KLK CGVS LD ++ Sbjct: 132 QYGVPWAYGTDGIGYNVQAVQKALGANAPVDSWALVFDPANLSKLKGCGVSILDQAVDVF 191 Query: 186 PAALHYLGYKPDTDNPKELKAAEELFLKIRPYVTYFHSSKYISDLANGNICVAIGYSGDI 245 A L Y+ P++ NP + +AA E+ KIRPY+T F+SS YI+DLAN ++CVA G+SGD+ Sbjct: 192 AATLQYMHKDPNSTNPADYQAAYEVLKKIRPYITQFNSSGYINDLANNDVCVAFGWSGDV 251 Query: 246 YQAKSRAEEAKNKVTVKYNIPKEGAGSFFDMVAIPKDAENTEGALAFVNFLMKPEIMAEI 305 A R EEAK +K++ KEG +FD++ IPKDA + E AL ++N++ P++ A I Sbjct: 252 GIASRRTEEAKRSYQIKFSNVKEGGLLWFDVMVIPKDAPHPEAALKWINYISDPKVNAAI 311 Query: 306 TDVVQFPNGNAAATPLVSEAIRNDPGIYPSEEVMKKLYTFPDLPAKTQRAMTRSWTKIKS 365 T+ V +P N AA V+ A+ D +YP +EV+ K+ +P R R W ++K+ Sbjct: 312 TNEVFYPTANKAARQFVTPAVAQDKTVYPGDEVLSKMTLMKPMPTDILRLENRLWAQLKT 371 Query: 366 G 366 G Sbjct: 372 G 372 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: 443 Number of extensions: 17 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: 373 Length adjustment: 30 Effective length of query: 337 Effective length of database: 343 Effective search space: 115591 Effective search space used: 115591 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