Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 3608585 Dshi_1979 inner-membrane translocator (RefSeq)
Query= TCDB::P74318 (286 letters) >FitnessBrowser__Dino:3608585 Length = 305 Score = 171 bits (434), Expect = 1e-47 Identities = 110/307 (35%), Positives = 173/307 (56%), Gaps = 39/307 (12%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAY----------------- 47 Q + +GI VG+I++LGA+GLTLT +LR +NF+H + +++ AY Sbjct: 3 QHLLDGILVGAILSLGAIGLTLTMHMLRFANFSHAELLSIGAYAALVFDALFSALLPALQ 62 Query: 48 -------LTWWANTSGINLWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISI 100 LTW + + + SMAL + I + L++K +R + +++ S Sbjct: 63 TAIPPLSLTWTLSLATV---ASMALTGLSAIAI----DRLIFKRVR-EKGGELSMVFASF 114 Query: 101 GLALFLRNGILLIWGGNNQNYRVPIVPA-----QDFMGIKFEYYRLLVIAMAIAAMVVLH 155 G+A+ +RN I L +G N Q Y IV A + +K + LV A+AI MVVLH Sbjct: 115 GVAMVIRNLIGLGFGLNTQLYSDDIVFATVLSRDPLILVKPDQVFTLVAALAI--MVVLH 172 Query: 156 LILQRTKVGKAMRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPN 215 L+L RT G ++RAVA+N LA+VSGIN++ +V W++ L A G YGL + P Sbjct: 173 LVLSRTTFGYSLRAVAENPVLAQVSGINLQRMVALIWILGGTLAAAAGVFYGLTNQITPV 232 Query: 216 MGWFLILPMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILF 275 +G L+LP+FA+ I+GGIG+ YGA+ GG ++G+A +++ + Y V L+++ +L Sbjct: 233 IGRDLVLPIFAATIVGGIGSIYGAVLGGFLVGIAANLALVVLPSGYSPSVPFLILVAVLV 292 Query: 276 IRPQGLF 282 +RP GLF Sbjct: 293 LRPHGLF 299 Lambda K H 0.329 0.143 0.450 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: 213 Number of extensions: 10 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: 286 Length of database: 305 Length adjustment: 26 Effective length of query: 260 Effective length of database: 279 Effective search space: 72540 Effective search space used: 72540 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 (21.8 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