Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate H281DRAFT_04062 H281DRAFT_04062 amino acid/amide ABC transporter membrane protein 1, HAAT family
Query= TCDB::P74318 (286 letters) >FitnessBrowser__Burk376:H281DRAFT_04062 Length = 316 Score = 139 bits (349), Expect = 1e-37 Identities = 93/307 (30%), Positives = 166/307 (54%), Gaps = 35/307 (11%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWA------NTSGIN 58 Q I NG+ +GS+ A+ A+G T+ YGIL + NFAHGD + + A + A + G+ Sbjct: 6 QQILNGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAIGVLQNHFPGLG 65 Query: 59 ----LWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIW 114 L +++A+ V + + E + ++P+R +A +I +IG+++ L+ ++IW Sbjct: 66 NVPTLCIALAIAAVVCAVVGYTIERVAYRPLR--KAPRLAPLITAIGVSILLQTLAMMIW 123 Query: 115 GGNNQNYR-------VPIVPAQDFM-GIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKA 166 N + + ++ A D G +++I +A M L L++ +TK+G+A Sbjct: 124 SRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMAGLLLLVHKTKLGRA 183 Query: 167 MRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSM----YGLMTTLKPNMGWFLIL 222 MRA+A+N +A + G+N +V+ T+++ + L AL G M YG MG+ L Sbjct: 184 MRAIAENPGVASLMGVNPNFVISATFMIGSALAALAGVMIASEYG---NAHFYMGFIPGL 240 Query: 223 PMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPW--------FGTSYKMGVALLLMIIIL 274 F + +LGGIGN GA+ GG+I+G+ +++ + FG++Y+ A +++II+L Sbjct: 241 KAFTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFAFIVLIIVL 300 Query: 275 FIRPQGL 281 RP GL Sbjct: 301 VFRPSGL 307 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: 14 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: 316 Length adjustment: 27 Effective length of query: 259 Effective length of database: 289 Effective search space: 74851 Effective search space used: 74851 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