Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate HSERO_RS04845 HSERO_RS04845 ABC transporter
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__HerbieS:HSERO_RS04845 Length = 366 Score = 361 bits (926), Expect = e-104 Identities = 199/360 (55%), Positives = 254/360 (70%), Gaps = 9/360 (2%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L L ++K VGA+T LY + L L G + VLLG TQAGKTSLMRI+AGLD PTAGRV VD Sbjct: 3 LELKQVAKTVGAETHLYPLDLNLAKGGINVLLGPTQAGKTSLMRIIAGLDKPTAGRVLVD 62 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLHI 120 G+DVTG+ VR+RN+AMVYQQFINYP + V NIA+PL+L+ E+ I RV+EIA +LHI Sbjct: 63 GQDVTGVGVRERNLAMVYQQFINYPGLTVFENIAAPLRLQKQPEQEISKRVKEIADKLHI 122 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 L R P ELSGGQQQR ALARAL K APL+LLDEPLVNLDYKLREELR EL LFA G Sbjct: 123 AHLLQRLPGELSGGQQQRCALARALIKRAPLVLLDEPLVNLDYKLREELRSELISLFATG 182 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240 +TVVYATTEP EALLLGG+TAV+ +G+LLQ+ PT E+F++P S +VA F+DPPMNL+ Sbjct: 183 DTTVVYATTEPQEALLLGGHTAVMHQGRLLQFAPTLELFNSPASTQVAAIFNDPPMNLLE 242 Query: 241 ASATAQ-----GVRLQGGAELTLP-LPQGAATAAGLTVGVRASALRVHARPG-DVSVAGV 293 A+A A + + G+ L + P + +G+R + +R+ A G VS+ Sbjct: 243 ATAIASAPGVAAICMSDGSVLEIAGRPLALSEGQSCKLGIRCNDVRLEALTGPGVSLGCS 302 Query: 294 VELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQAP 353 V LAE+SGS+T++H LVAQL+GVH +G+ + + + A+A++F GRL AP Sbjct: 303 VTLAELSGSETYLHLRHGEVPLVAQLSGVHEVAIGSTVQVSIAAAKAFLFDTQGRLLSAP 362 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: 380 Number of extensions: 15 Number of successful extensions: 3 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: 366 Length adjustment: 29 Effective length of query: 334 Effective length of database: 337 Effective search space: 112558 Effective search space used: 112558 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