Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate AZOBR_RS27980 AZOBR_RS27980 sugar ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__azobra:AZOBR_RS27980 Length = 360 Score = 197 bits (502), Expect = 3e-55 Identities = 124/306 (40%), Positives = 178/306 (58%), Gaps = 21/306 (6%) Query: 7 DLAHSYKPNPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVL 66 DL SY P L + ++ DG AL+GPSGCGK+T+L +++GL G++ Sbjct: 8 DLRKSYGGTP------VLHGVSVDIADGEFVALVGPSGCGKSTLLRMIAGLEEAGEGEIR 61 Query: 67 FDGRDVTRASPQERNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEML 126 GR V P++R+IA VFQ +Y MTVA+NL F L + V G+I RV AE+L Sbjct: 62 IGGRLVNDVPPKDRDIAMVFQNYALYPHMTVAQNLGFALTLKDVDRGEIAARVARAAEVL 121 Query: 127 EMSGQLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIH 186 +S L++R L+ +Q++++GR +VR D LFDEPL+ +D L+ Q+R ++K +H Sbjct: 122 GLSALLDRRPGQLSGGQRQRVAMGRAIVR-DPRLFLFDEPLSNLDAKLRVQMRAEIKALH 180 Query: 187 HELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMN 246 L+ + IYVTHDQ+EA+T AD++VVM G+ Q G+ L++RPA+ FV FIGSP MN Sbjct: 181 QRLRTSAIYVTHDQIEAMTMADRIVVMRDGRVEQAGAPLDLYDRPANRFVAGFIGSPAMN 240 Query: 247 FLPAHRDGENLSVAGHRLASPVGRALPAGALQ---------VGIRPEYLALAQPQQAGAL 297 FL R N A RL G LP A+ +G+RPE+ AL P++ L Sbjct: 241 FLTG-RIAVN-GRASFRLDG--GPDLPLSAVPLEADGRPAVLGLRPEH-ALIDPEEGVPL 295 Query: 298 PGTVVQ 303 VV+ Sbjct: 296 HVAVVE 301 Lambda K H 0.320 0.136 0.395 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: 311 Number of extensions: 15 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: 358 Length of database: 360 Length adjustment: 29 Effective length of query: 329 Effective length of database: 331 Effective search space: 108899 Effective search space used: 108899 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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