Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate BWI76_RS05365 BWI76_RS05365 D-methionine ABC transporter, ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Koxy:BWI76_RS05365 Length = 343 Score = 288 bits (738), Expect = 1e-82 Identities = 160/341 (46%), Positives = 221/341 (64%), Gaps = 8/341 (2%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 MI+ + K ++ R I AL L++ AGQI+G+IG SGAGKSTL+R +N LE P+ G Sbjct: 1 MIKLSKITKVFQQGNRSIQALNDVSLHVPAGQIYGVIGASGAGKSTLIRCVNLLERPTQG 60 Query: 61 RILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDA 120 + V G+++TAL + L R R+++GMIFQHFNLL+S+TV N+A+PL L + E+ Sbjct: 61 SVQVGGQELTALSEKELTRARRQIGMIFQHFNLLASRTVFGNVALPLEL-DNTPKEEIKR 119 Query: 121 RVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASV 180 RV+ELL VGL D YPA LSGGQKQRV IARALA P +LLCDEATSALDP TT S+ Sbjct: 120 RVTELLDLVGLGDKHDSYPANLSGGQKQRVAIARALASNPKVLLCDEATSALDPATTRSI 179 Query: 181 LQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRR 240 L+LL +INR L LTI+LITHEMDV++R+CD VAV+ G ++EQ V++VF HP+ P ++ Sbjct: 180 LELLKDINRRLGLTILLITHEMDVVKRICDCVAVISNGQLIEQDTVSEVFSHPKTPLAQQ 239 Query: 241 FVFEAERVDEDERHDDFAHVPGL-----ILRLTFRGEATYAPLLGTVARQTGVDYSILSG 295 F+ +D + + L +LR+ F G + APLL AR+ V+ +I+S Sbjct: 240 FIQSTLHLDIPDDYQARLKSEALPDSVPMLRMEFTGHSVDAPLLSETARRFNVNNNIISA 299 Query: 296 RIDRIKDTPYGQLTLALVG--GDLEAAMSQLNAADVHVEVL 334 ++D +G + + G D +AA++ L V VEVL Sbjct: 300 QMDYAGGVKFGIMLTEMHGTQEDTQAAIAWLQEHHVKVEVL 340 Lambda K H 0.322 0.138 0.393 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: 305 Number of extensions: 10 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: 335 Length of database: 343 Length adjustment: 28 Effective length of query: 307 Effective length of database: 315 Effective search space: 96705 Effective search space used: 96705 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 (21.9 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