Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate BPHYT_RS33300 BPHYT_RS33300 ABC transporter
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__BFirm:BPHYT_RS33300 Length = 368 Score = 369 bits (946), Expect = e-107 Identities = 205/361 (56%), Positives = 256/361 (70%), Gaps = 8/361 (2%) Query: 1 MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 M L L+ ++ GAQT LY + L L GA+ VLLG TQAGKT+LMR+MAGLD P +GRV Sbjct: 1 MVLELERVTVVSGAQTHLYGVDLRLVPGAINVLLGPTQAGKTTLMRVMAGLDRPASGRVL 60 Query: 61 VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEK--NIDARVREIASRL 118 DG DVTG+ VR RN+AMVYQQFINYP+M V NIASPL L+ + RV E+A++L Sbjct: 61 ADGNDVTGVSVRQRNLAMVYQQFINYPAMTVFDNIASPLNLQKTPADEVKRRVHEVAAKL 120 Query: 119 HIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA 178 HID L R P ELSGGQQQR ALARAL K + L+LLDEPLVNLDYKLREELR EL LFA Sbjct: 121 HIDHLLQRRPGELSGGQQQRCALARALVKRSSLVLLDEPLVNLDYKLREELRVELATLFA 180 Query: 179 AGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNL 238 G++TVVYATTEP EALLLGGYTA++D+G +LQ+GPT +V++AP ++ VA F+DPPMN+ Sbjct: 181 DGKTTVVYATTEPLEALLLGGYTAIVDKGCVLQHGPTLDVYNAPANIDVAAVFNDPPMNM 240 Query: 239 MAASATAQG-VRLQGGAELTLPLPQGAATAAGLT--VGVRASALRVHAR-PGDVSVAGVV 294 +A+ TA G RL G ++ L A T +GVR LR+ R P V+V + Sbjct: 241 LASDLTADGTARLPIGIDVPLGRASARAVRENETFRIGVRPGHLRLAPRTPRSVAVPCRL 300 Query: 295 ELAEISGSDTFVHASTPWG--DLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQA 352 ELAE+SGS+T++H T G DLVAQL GVH +LGT + +++DP + +VFGAD L Sbjct: 301 ELAELSGSETYLHLHTRQGGIDLVAQLQGVHQIDLGTELDVYIDPDELFVFGADTTLVSG 360 Query: 353 P 353 P Sbjct: 361 P 361 Lambda K H 0.318 0.133 0.375 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: 390 Number of extensions: 18 Number of successful extensions: 4 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: 363 Length of database: 368 Length adjustment: 30 Effective length of query: 333 Effective length of database: 338 Effective search space: 112554 Effective search space used: 112554 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 (21.7 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