Align D-methionine ABC transporter membrane protein, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate AO353_22195 AO353_22195 metal ABC transporter permease
Query= TCDB::Q9HT69 (225 letters) >FitnessBrowser__pseudo3_N2E3:AO353_22195 Length = 223 Score = 213 bits (541), Expect = 3e-60 Identities = 111/213 (52%), Positives = 154/213 (72%), Gaps = 4/213 (1%) Query: 11 NIDWYEIWL----ASVDTFWMLGGSLLFTVVLGLPLGVLLFLTGPRQMFEQKAVYTLLSL 66 +IDW EI A+ +T +M+ + FT+++GLPLGVLLF++ ++ + L Sbjct: 4 SIDWNEILQLVLNATGETLYMVLLAGFFTLLIGLPLGVLLFISRSGGLYPMPKLNKGLGG 63 Query: 67 VVNILRSLPFIILLIVMIPLTVLITGTSLGVAGAIPPLVVGATPFFARLVETALREVDKG 126 +VN+ RSLPF+++LI +IPLT LI GT+LG A+ P+ +GA PFFAR+VE AL EVDKG Sbjct: 64 LVNLGRSLPFVVMLIALIPLTRLIVGTTLGSTAAVVPITIGAFPFFARIVENALDEVDKG 123 Query: 127 IIEATQAMGASTRQIIWNALLPEARPGIIAAITVTAITLVSYTAMAGVVGAGGLGDLAIR 186 IEA AMG R +I+ LLPEA P ++A IT+T + L+ +++MAGV+G GGLGDLAIR Sbjct: 124 RIEAILAMGGDIRHVIFKVLLPEALPALLAGITLTLVMLIGFSSMAGVIGGGGLGDLAIR 183 Query: 187 FGYQRFQTDVMVVTVVMLLILVQILQTVGDKLV 219 +GYQRF VMV TVV+L+ILVQ +Q++GD+LV Sbjct: 184 YGYQRFNNQVMVATVVVLVILVQGVQSLGDRLV 216 Lambda K H 0.329 0.143 0.419 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: 123 Number of extensions: 8 Number of successful extensions: 1 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: 225 Length of database: 223 Length adjustment: 22 Effective length of query: 203 Effective length of database: 201 Effective search space: 40803 Effective search space used: 40803 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 46 (22.3 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