Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate PfGW456L13_386 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_386 Length = 254 Score = 245 bits (625), Expect = 8e-70 Identities = 129/247 (52%), Positives = 177/247 (71%), Gaps = 3/247 (1%) Query: 16 LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75 L + +LHK YG EVLKGV L + G+V++LIG+SGSGK+T LRC+N LE G + LD Sbjct: 4 LTVENLHKSYGNHEVLKGVSLNARTGDVISLIGASGSGKSTFLRCINFLETPNDGAMSLD 63 Query: 76 GESIGY-HEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLHK 134 + I H+ +G RV + + + + R M FQ FNL+ H+T L N+T+ +V + K Sbjct: 64 SQPIKMVHDHHGMRVADANE-LQRIRTRLAMVFQHFNLWSHMTVLDNITMAPRRVLGVSK 122 Query: 135 DEAVVLAEKWLERVGLLER-RDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDP 193 +A A ++L++VGL R D YP LSGGQQQRVAIARA++M P +MLFDE TSALDP Sbjct: 123 KDAEDRARRYLDKVGLPARVADQYPAFLSGGQQQRVAIARALSMEPEIMLFDEPTSALDP 182 Query: 194 ELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERPQS 253 ELVGEVL VI+GLAE+G TM++VTHEM FA +VS++++F++QGR+EEQG P+++ P+S Sbjct: 183 ELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGRVEEQGAPEDVLGNPKS 242 Query: 254 PRLAEFL 260 RL +FL Sbjct: 243 ERLKQFL 249 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: 186 Number of extensions: 9 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: 265 Length of database: 254 Length adjustment: 24 Effective length of query: 241 Effective length of database: 230 Effective search space: 55430 Effective search space used: 55430 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: 47 (22.7 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