Align Solute-binding protein Bpro_3107 (characterized)
to candidate AZOBR_RS26640 AZOBR_RS26640 ABC transporter substrate-binding protein
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__azobra:AZOBR_RS26640 Length = 339 Score = 180 bits (457), Expect = 4e-50 Identities = 105/314 (33%), Positives = 171/314 (54%), Gaps = 4/314 (1%) Query: 7 RISAIRSAALAALLAGLGMGAAQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHK 66 + S I + A+AAL A A A A D+P A V + +KSGGK K Sbjct: 5 KFSIILTVAVAALFAAAPAKAQTAERTMRLSAAVAQDHPFAAGVSALTACAAEKSGGKMK 64 Query: 67 IKVFNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSL 126 I+ F ALGS+ + + V+ G+LD + P+ ++ P V +PFLF + + L Sbjct: 65 IQSFWNAALGSDMQAVQLVRGGSLDMVVASTSPLASLVPAMGVFDLPFLFENETEADRIL 124 Query: 127 DGPVGDEILKSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVALV 185 DG VG ++ + + G + LA++++G R++ +++PI+ D G KIRV Q+ +++ Sbjct: 125 DGAVGQQLSEKLQGVGLVNLAYWENGFRNLTNSRRPIQKWEDLGGTKIRVMQNPVFMDTF 184 Query: 186 SAMGANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVM 245 S +GANA PM + E++T L+T +D EN + +T K EA K S T H+ P +++ Sbjct: 185 STLGANAVPMAFSELFTALETRAVDGQENPYANIETGKFYEAQKYLSVTNHAYTPAVILY 244 Query: 246 SKIIYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEV---DKKSF 302 SK I+D L AE+D++++ A + ER+ EQ KSLA +K G ++ E+ ++K Sbjct: 245 SKKIWDGLSSAERDVLQSCAAVARTEERRVNREQSEKSLARLKDLGMQVNELSAEERKRM 304 Query: 303 QAVMGPVYDKFMTT 316 + PVY+K T Sbjct: 305 LQKVAPVYEKHAAT 318 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: 208 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