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 5210165 Shew_2609 inner-membrane translocator (RefSeq)
Query= TCDB::Q8YXD0 (288 letters) >FitnessBrowser__PV4:5210165 Length = 297 Score = 125 bits (314), Expect = 1e-33 Identities = 86/292 (29%), Positives = 157/292 (53%), Gaps = 22/292 (7%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGA-----YLTFFVNTFGVN 60 IQLI+NG+ VG + + + L Y ++ NFA G+FL +GA +LT+F F V Sbjct: 7 IQLIINGLIVGLLYGVVGMCFVLVYKSTQIVNFAQGEFLLVGAWVCWAFLTYFQLPFFVG 66 Query: 61 IWLSM-IVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGR 119 ++ +AV G + M++ ++ + S+ I+++IGL++F ++ I+G Sbjct: 67 FLFTLCFMAVFGVLLQMIVLRPMIGEPIISV-------IMVTIGLSIFFQSLTKWIFGVS 119 Query: 120 NQNYNLPI-TPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDL 178 Q+Y T ++ IFG+ + L+ +A+L + A + +K G AMRA A D + Sbjct: 120 PQSYPQVFDTQSIAIFGLNIELAYLMSTVIAILIMAAFFLFFKYSKHGLAMRATAFDQQV 179 Query: 179 AKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNP 238 A+ GI V+QV +W IA TV++ G + G++ V ++ + + +F +VILGG+ + Sbjct: 180 AQSLGISVKQVFAMSWGIAATVSATAGVVIGMVNGVSDSLS-TIGIKVFPAVILGGLDSI 238 Query: 239 YGAIAAAFIIGIVQEVSTPF------LGSQYKQGVALLIMILVLLIRPKGLF 284 GAI +IG+++ ++ F +G+ Y +++++L +P GLF Sbjct: 239 VGAIVGGVVIGVLENIAEFFDSQWLHIGNMY-DIAPFYVLLVILWFKPYGLF 289 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: 280 Number of extensions: 13 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: 288 Length of database: 297 Length adjustment: 26 Effective length of query: 262 Effective length of database: 271 Effective search space: 71002 Effective search space used: 71002 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