Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= reanno::pseudo6_N2E2:Pf6N2E2_2050 (263 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 138 bits (347), Expect = 2e-37 Identities = 83/247 (33%), Positives = 136/247 (55%), Gaps = 16/247 (6%) Query: 13 LLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIML 72 ++++ + K +G L V L++++G VT++G SG GKTTLLR + + G+I + Sbjct: 9 IIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRI 68 Query: 73 DGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPK 132 G+ I + P H+ FQ++ LFPHL N+ GL K+KK PK Sbjct: 69 SGKEI---------TQTPP-----HKRPVNTVFQKYALFPHLNVYDNIAFGL-KLKKTPK 113 Query: 133 DEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 192 + L+ VG+ + LSGGQQQRVAIARAI P ++L DE +ALD + Sbjct: 114 QTIGKKVKAALKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLK 173 Query: 193 LVGEVLNVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 251 + ++ +K + + G+T + VTH+ A +SD IV M++G+I++ G P +++ P + Sbjct: 174 MRKDMQMELKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPIN 233 Query: 252 PRLAEFL 258 +A+F+ Sbjct: 234 SFVADFI 240 Lambda K H 0.320 0.138 0.392 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: 275 Number of extensions: 8 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: 263 Length of database: 463 Length adjustment: 29 Effective length of query: 234 Effective length of database: 434 Effective search space: 101556 Effective search space used: 101556 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 Apr 09 2024. 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