Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 157 bits (397), Expect = 4e-43 Identities = 117/327 (35%), Positives = 171/327 (52%), Gaps = 33/327 (10%) Query: 1 MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 M +A+ S+ K+ G L + L + G + LLG + +GKT+L+R +AGL+ P AG+V Sbjct: 1 MTIAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVL 60 Query: 61 VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKN------IDARVREI 114 DG+DVT R V V+QQ+ + M VA NIA L +R K+ I RV E+ Sbjct: 61 FDGQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEEL 120 Query: 115 ASRLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELT 174 + ++ RYP++LSGGQ+QRVAL+RALA ++LLDEP LD +R+ LR EL Sbjct: 121 LKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELR 180 Query: 175 QLFAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDP 234 ++ A T ++ T + EAL L A+L+ G++ Q G +V AP + V + Sbjct: 181 RVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVGE- 239 Query: 235 PMNLMAASATAQGVRLQGGAELTLP---LPQGAATAAGLTVGVRASALRVHARPGDVSV- 290 G R + GA LT+P L GAATA + RP D ++ Sbjct: 240 ---ANRFDGQVSGGRFKAGA-LTVPASALKDGAATA--------------YVRPHDFALD 281 Query: 291 -AG---VVELAEISGSDTFVHASTPWG 313 AG ++E A++ G+ T V A T G Sbjct: 282 EAGFEVLIERAQVQGALTAVTALTSDG 308 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: 249 Number of extensions: 8 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: 363 Length of database: 339 Length adjustment: 29 Effective length of query: 334 Effective length of database: 310 Effective search space: 103540 Effective search space used: 103540 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