Align Solute-binding protein Bpro_3107 (characterized)
to candidate AO356_25645 AO356_25645 ABC transporter substrate-binding protein
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25645 Length = 339 Score = 171 bits (434), Expect = 2e-47 Identities = 108/313 (34%), Positives = 167/313 (53%), Gaps = 10/313 (3%) Query: 13 SAALAALLAGLGMGAAQATEFRSADTH----NADDYPTVAAVKYMGELLEKKSGGKHKIK 68 + A LL G+ A+ A E R N ++P + +LL +KSGGK K++ Sbjct: 12 ACATGLLLTGV---ASHADEIRERTLRFAFQNVKEHPQGQGAQKFADLLSEKSGGKIKVR 68 Query: 69 VFNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLDG 128 +F LG + +T+ ++ G LD T +N G + A P + PFLF+++ +DG Sbjct: 69 LFPGGTLGGDVQTVSALQGGTLDITVLNSGILAAQAPDYAMLDFPFLFNNVEEAHAVIDG 128 Query: 129 PVGDEILKSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVALVSA 187 PVG ++ +S G +GL ++D G R++ +K P+ + D +GLKIRV QS +++ SA Sbjct: 129 PVGQKLAAQLDSKGLVGLGYWDLGFRNLTNSKHPVTKLEDMQGLKIRVIQSPIYLETFSA 188 Query: 188 MGANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMSK 247 +GAN PM + EVYTGL+ ID EN + K E K S T H P+ L++S+ Sbjct: 189 LGANPVPMAFPEVYTGLEQHTIDGQENPFTVIEGNKFYEVQKYLSVTGHIFNPQSLIISQ 248 Query: 248 IIYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGA--EIVEVDKKSFQAV 305 +++L E+ MIRAAA E+ AF+R+ K+ A + AA EI +K + Sbjct: 249 KTWNRLNDDEKAMIRAAAAEAQAFQREVTAASMDKAKATLAAAMTVNEITPAEKDRLRER 308 Query: 306 MGPVYDKFMTTPD 318 + PV DKF + D Sbjct: 309 VKPVVDKFAKSLD 321 Lambda K H 0.316 0.130 0.362 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: 210 Number of extensions: 7 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: 330 Length of database: 339 Length adjustment: 28 Effective length of query: 302 Effective length of database: 311 Effective search space: 93922 Effective search space used: 93922 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