Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 3608113 Dshi_1518 inner-membrane translocator (RefSeq)
Query= TCDB::P74318 (286 letters) >FitnessBrowser__Dino:3608113 Length = 336 Score = 174 bits (442), Expect = 2e-48 Identities = 118/325 (36%), Positives = 181/325 (55%), Gaps = 45/325 (13%) Query: 3 LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFM---TLAAYLTWWANTS-GIN 58 L+ ++ A GS +ALGA+G+TL YGILR SNFAHGD M T+A L WA S GI+ Sbjct: 11 LNFVVVPATAYGSQLALGALGVTLIYGILRFSNFAHGDTMAFGTMATILFTWAFQSIGIS 70 Query: 59 LW------LSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGIL- 111 L L++ G + T + + L++K R ++A +I S+G+ +F+ N ++ Sbjct: 71 LGPLPTALLALPFGILVTGALLVGTDRLVYKFYRQQKAVPVIFVIASLGV-MFVTNALVR 129 Query: 112 LIWGGNNQNYRVP---IVPAQDFM-------GIKFEYYRLLVIAMAIAAMVVLHLILQRT 161 I G ++Q + I+ A++F G+ + L + A+ + +L L RT Sbjct: 130 FIIGPDDQRFADGERFIISAREFRNLTGLDEGLALRTTQGLTVVTAVIVVALLFWFLNRT 189 Query: 162 KVGKAMRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLI 221 + GK+MRA +DN DLA +SGIN E VVM TW++ A L + G++YGL + KP + L+ Sbjct: 190 RTGKSMRAFSDNEDLALLSGINPERVVMVTWLIVAALATVAGTLYGLDKSFKPFTYFQLL 249 Query: 222 LPMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPW----------------------FGT 259 LP+FA+ I+GG+G+P GAIAGG +I + EV++ + T Sbjct: 250 LPIFAAAIVGGLGSPLGAIAGGFVIAFS-EVTITYAFKKVLEYLLPEALEPDGLVQLLST 308 Query: 260 SYKMGVALLLMIIILFIRPQGLFKG 284 YK V+ ++II+L +P GLFKG Sbjct: 309 DYKFAVSFAILIIVLLFKPTGLFKG 333 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: 255 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: 286 Length of database: 336 Length adjustment: 27 Effective length of query: 259 Effective length of database: 309 Effective search space: 80031 Effective search space used: 80031 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