Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate Echvi_1582 Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Cola:Echvi_1582 Length = 225 Score = 145 bits (366), Expect = 9e-40 Identities = 80/224 (35%), Positives = 127/224 (56%), Gaps = 5/224 (2%) Query: 1 MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60 ++ +V K Y+ R + L+ L+++AG ++G SG+GK+TLL L L+ S G Sbjct: 3 ILSIENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSASSG 62 Query: 61 RILVEGEDVTALDAEGLRRFR-QRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVD 119 + + G + L + R Q +G IFQ+F LL + T +N+ +PL L R + Sbjct: 63 SVALNGHRLEGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALENVMVPLELK---KRKDAK 119 Query: 120 ARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTAS 179 + +ELL +VGL D YP QLSGG++QRV IARA A P IL DE T LD +T Sbjct: 120 QKATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTETGEL 179 Query: 180 VLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQ 223 + L+ ++N+ L T++L+TH+ D+ + +++ + GG I E+ Sbjct: 180 IETLIFDLNKALGTTLILVTHDTDLAAKT-NRIIHIKGGKIQEE 222 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: 185 Number of extensions: 11 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: 225 Length adjustment: 25 Effective length of query: 310 Effective length of database: 200 Effective search space: 62000 Effective search space used: 62000 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: 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