Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 153 bits (387), Expect = 4e-42 Identities = 89/249 (35%), Positives = 138/249 (55%), Gaps = 18/249 (7%) Query: 16 LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75 + IR + KQ+G L VDL + G ++ L+G SGSGKTTLLR + LE GQ+L D Sbjct: 3 IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62 Query: 76 GESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHKD 135 G+ + Y +RV G FQQ+ LF H+T +N+ GL K K Sbjct: 63 GQDVTYASAAARRV--------------GFVFQQYALFKHMTVAKNIAFGLDVRKGKDKP 108 Query: 136 EAVVLAEKWLERVGLLERR---DHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 192 +A + E + L+E YP QLSGGQ+QRVA++RA+A+ PS++L DE ALD Sbjct: 109 SKAEIARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALD 168 Query: 193 PELVGEVLSVIKGLAE-DGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERP 251 + + ++ + + G+T + VTH+ A E++D++ +N GRIE+ G P ++ + P Sbjct: 169 ATVRKSLRRELRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAP 228 Query: 252 QSPRLAEFL 260 ++ + F+ Sbjct: 229 ETAFVCGFV 237 Lambda K H 0.319 0.135 0.379 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: 196 Number of extensions: 10 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: 265 Length of database: 339 Length adjustment: 27 Effective length of query: 238 Effective length of database: 312 Effective search space: 74256 Effective search space used: 74256 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: 48 (23.1 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