Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate SM_b20604 SM_b20604 branched-chain amino acid ABC transporter permease
Query= TCDB::P74318 (286 letters) >FitnessBrowser__Smeli:SM_b20604 Length = 537 Score = 133 bits (335), Expect = 8e-36 Identities = 90/296 (30%), Positives = 153/296 (51%), Gaps = 28/296 (9%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWAN----TSGINLW 60 Q I+ G+++GS++ L A+GL +T+G++ + N AHG+ + L AY T+ TS +L+ Sbjct: 243 QNIWYGLSLGSVLLLAAIGLAITFGVMGIINMAHGEMVMLGAYTTFLVQDVVRTSFPHLF 302 Query: 61 ---LSMAL-------GCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGI 110 L++AL G VG + + +L +P+ AT G++L L+ + Sbjct: 303 EWSLAIALPLAFLVTGAVGLALERGVIRFLYGRPLETLLATW--------GISLILQQTV 354 Query: 111 LLIWGGNNQNYRVP--IVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMR 168 I+G N+ P + A + G+ + RL +I A+A L +L++T +G MR Sbjct: 355 RTIFGPTNREVGNPSWMSGAFELGGLAITWNRLWIIVFALAVFAALLFLLKKTPMGLQMR 414 Query: 169 AVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASV 228 AV N +A GI WV T+ + + + + G + + PN+G I+ F V Sbjct: 415 AVTQNRRMASSMGIRTPWVDALTFALGSGIAGIAGVALSQIDNVSPNLGQGYIIDSFMVV 474 Query: 229 ILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFI--RPQGLF 282 + GG+GN +G + G +G+ + P+ G +G L+L++IILFI RP+GLF Sbjct: 475 VFGGVGNLWGTLVGAFSLGILNKFLEPYAGA--VLGKILVLVLIILFIQKRPRGLF 528 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: 380 Number of extensions: 17 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: 286 Length of database: 537 Length adjustment: 31 Effective length of query: 255 Effective length of database: 506 Effective search space: 129030 Effective search space used: 129030 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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