Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate CCNA_01506 CCNA_01506 cystine transport ATP-binding protein
Query= TCDB::Q9HT70 (335 letters) >FitnessBrowser__Caulo:CCNA_01506 Length = 246 Score = 152 bits (385), Expect = 6e-42 Identities = 92/235 (39%), Positives = 133/235 (56%), Gaps = 4/235 (1%) Query: 9 KTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGED 68 K+ + + + P L L + G++ +IG SG+GKSTLLR + LE + G + + G Sbjct: 7 KSLKKSFGDTPVLAGVDLAVVPGEVVAIIGPSGSGKSTLLRCLAGLEPLNDGDLTIAG-- 64 Query: 69 VTALDAEGLRR-FRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLA 127 V A L + RVG +FQ FNL +T +N+ + A+ A+ LL Sbjct: 65 VAAGGKTPLAKALNGRVGFVFQSFNLFPHRTALENVIEGPIVVRREDPAKARAKGLALLE 124 Query: 128 RVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEI 187 +VGL+D YP+ LSGGQ+QR IARALA P ++L DE TSALDP+ VL ++ ++ Sbjct: 125 KVGLADRVDAYPSALSGGQQQRCAIARALAMDPEVILFDEPTSALDPELVGEVLAVIRDL 184 Query: 188 NRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242 E K T+V++TH+MD R V ++ MDGG IVEQG + P+ TRRF+ Sbjct: 185 AAE-KRTMVIVTHQMDFARDVAERTIFMDGGVIVEQGPSRQLLASPREERTRRFL 238 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: 233 Number of extensions: 10 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: 335 Length of database: 246 Length adjustment: 26 Effective length of query: 309 Effective length of database: 220 Effective search space: 67980 Effective search space used: 67980 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