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 WP_017540507.1 C892_RS0115120 hypothetical protein
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_000341205.1:WP_017540507.1 Length = 470 Score = 189 bits (479), Expect = 1e-52 Identities = 114/299 (38%), Positives = 176/299 (58%), Gaps = 24/299 (8%) Query: 7 QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFF------------- 53 QL V G+ G IIA+++VGL+L +G R+ NFAHGD +T GA++ Sbjct: 166 QLTVAGLTFGLIIAISSVGLSLIFGTTRMINFAHGDMVTFGAFMAMMFANMTLFSSLHEV 225 Query: 54 -----VNTFGVN-IWLSMIVAVV--GTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLA 105 V F N + L +++AVV G +G L E+ LW +R + I++IG + Sbjct: 226 FEGVPVLDFVFNPLVLGLVLAVVLGGALGAGL--ERFLWRPLRRRNVALIQMFIVTIGFS 283 Query: 106 LFLRNGIILIWGGRNQNY-NLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTK 164 L LR+ +++++G R Y I A ++ V + +L +AV+ + + +LQ T+ Sbjct: 284 LVLRHMLLVVFGARRDKYPQFRIQEAWELGPVSITPRDAGILLVAVVVLVLVASMLQFTR 343 Query: 165 IGKAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLIL 224 +GKAMRAVAD+ DLA+ SGIDV++V + W + G +++LGG +YGL V MG+ L+L Sbjct: 344 MGKAMRAVADNRDLAESSGIDVDRVTLYVWGLGGALSALGGVLYGLNATVHWQMGFHLLL 403 Query: 225 PLFASVILGGIGNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283 +FA+VILGG+G YGA+ ++G+V +ST + Q AL IMILVLL+RP+G+ Sbjct: 404 LMFAAVILGGLGTAYGAMVGGLVVGLVAMLSTLWFSPQLMNVWALGIMILVLLVRPQGI 462 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: 333 Number of extensions: 17 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: 288 Length of database: 470 Length adjustment: 30 Effective length of query: 258 Effective length of database: 440 Effective search space: 113520 Effective search space used: 113520 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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