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) >lcl|FitnessBrowser__Smeli:SM_b20604 SM_b20604 branched-chain amino acid ABC transporter permease 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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