Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__SynE:Synpcc7942_2495 Length = 313 Score = 139 bits (349), Expect = 1e-37 Identities = 91/305 (29%), Positives = 164/305 (53%), Gaps = 29/305 (9%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFV----------- 54 +Q ++NG+A+G + AL A+G TL + IL + NFAHG TLGAYLT+ + Sbjct: 4 LQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLGAYLTYALVGGRFSFNGLL 63 Query: 55 ----NTFGVNIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRN 110 F + L++++ + G LL E++ + +R +A+ +I S+G+A+F+ N Sbjct: 64 ANAALPFSLPFALALLLGSLLAGGASLLIEQVAFRPLRRRQADPLLTLISSLGVAVFIVN 123 Query: 111 GIILIWGGRNQNYNLP------ITPALDIFG----VKVPQNQLLVLALAVLSIGALHYLL 160 I ++ G + Y P + A+++ +++ Q+++ +A+ L +L+ Sbjct: 124 LIQILVGA--EIYTFPSNIYGDLPSAINLGSSDRPIQIRTVQIILFVVAIAMFSLLTWLI 181 Query: 161 QNTKIGKAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGL-ITAVRPNMG 219 T++G A++AVA+D A + GID ++ I T+ ++G + L G++ G ++ P G Sbjct: 182 NGTRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPYFG 241 Query: 220 WFLILPLFASVILGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIR 279 L + ++LGG+GN G IA ++G+ E P S Y+ VA ++ +LLIR Sbjct: 242 IAYGLKGLSVMVLGGLGNIPGTIAGGLLLGLA-EAWVPPQWSGYRDAVAFALLFAMLLIR 300 Query: 280 PKGLF 284 P+GLF Sbjct: 301 PQGLF 305 Lambda K H 0.328 0.144 0.426 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: 276 Number of extensions: 23 Number of successful extensions: 5 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: 288 Length of database: 313 Length adjustment: 27 Effective length of query: 261 Effective length of database: 286 Effective search space: 74646 Effective search space used: 74646 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 (21.7 bits) S2: 48 (23.1 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