Align NatC, 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_1894 Synpcc7942_1894 integral membrane protein of the ABC-type Nat permease for neutral amino acids
Query= TCDB::Q8YY08 (377 letters) >FitnessBrowser__SynE:Synpcc7942_1894 Length = 359 Score = 353 bits (907), Expect = e-102 Identities = 190/383 (49%), Positives = 262/383 (68%), Gaps = 30/383 (7%) Query: 1 MIEYLIFLAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLKGVPLFIS 60 MI Y+I L + A FALF +GLNL WG+TGL+NFGH+AF+ +GAY+ LL+ +G PL+++ Sbjct: 1 MIGYIILLVCTIALFALFCVGLNLHWGYTGLLNFGHVAFLLIGAYSVSLLAQQGWPLWLA 60 Query: 61 AIVGAIFAALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGV 120 AI G AALLGLV+G A+LRL +DYL IVT+G E++R+ V N+ G T G+FGV Sbjct: 61 AIAGVTLAALLGLVMGVASLRLSQDYLGIVTVGLAEVLRIFVQNE---TGLT--QGSFGV 115 Query: 121 QSYPIPLST-EPNLF-FRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQE 178 Q+YPI L EP ++ LL++G+L + A + LW+W R++ Sbjct: 116 QAYPIILQGWEPPIWQTHLLVVGLLAIA-AWGYWQLWQWWRSS----------------- 157 Query: 179 IASRFGVGIILGLLATAIYISGVITL----YNYIPKAGLMLVSLLVLAFVFWRLEYLVRS 234 ASR + + L +++ + L Y P++G ML+ L L ++ LVRS Sbjct: 158 -ASRGKHWLAIVALGSSLIVLPPAALGLADYERYPRSGQMLLLLGALWLTVAAVDRLVRS 216 Query: 235 PWGRVLKAIREDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQ 294 PWGRVLKAIREDE + A+GKNV YKLQSL LGGAIAG+AG F+AWQ++AIYPDNF+PQ Sbjct: 217 PWGRVLKAIREDETVAIALGKNVLSYKLQSLALGGAIAGLAGVFYAWQLTAIYPDNFRPQ 276 Query: 295 LTFDSWIMVILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLI 354 LTFD W M++LGG + G +LGA +++ YD++TR +LP I+PLD +++GA RI +GL+ Sbjct: 277 LTFDVWTMLVLGGTAHRFGPVLGAAVFWLYDSLTRFLLPAILPLDGSQIGALRIALVGLL 336 Query: 355 LMVLMIWRPQGILGKKEELTLGK 377 LM LMIWRPQGILG++EEL+LG+ Sbjct: 337 LMALMIWRPQGILGRREELSLGR 359 Lambda K H 0.328 0.145 0.441 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: 532 Number of extensions: 20 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: 377 Length of database: 359 Length adjustment: 30 Effective length of query: 347 Effective length of database: 329 Effective search space: 114163 Effective search space used: 114163 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 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