Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_013403235.1 CALHY_RS06825 branched-chain amino acid ABC transporter permease
Query= TCDB::P74318 (286 letters) >NCBI__GCF_000166355.1:WP_013403235.1 Length = 294 Score = 153 bits (386), Expect = 5e-42 Identities = 94/284 (33%), Positives = 164/284 (57%), Gaps = 11/284 (3%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS-GINLWLSM 63 Q + NGI +GS+ AL ++G T+ YGI++L NFAHGD + AY+ + + T + L S+ Sbjct: 6 QQLINGITLGSVYALISLGYTMVYGIIKLINFAHGDIFMVGAYIAYLSVTYLKLGLIPSL 65 Query: 64 ALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGNNQNYRV 123 + V I + E +KP+R + + +I +IG++L L N + +I G +++ + Sbjct: 66 IVSMVFCSILGMLIEKFAYKPLR--NSPRISALITAIGVSLLLENLMQIIMGADSRVFPR 123 Query: 124 PIVPA-----QDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDLAK 178 + QD + + + LL+I + + M++L+ ++++TK+GKAMRAV+ ++D A+ Sbjct: 124 LVAEKNYHLFQDRIVVNNKQIYLLIITVLL--MIILNFVVKKTKIGKAMRAVSQDMDAAR 181 Query: 179 VSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVILGGIGNPY 237 + GINV+ + +T+ + + L A G + GL T+ P MG L F + + GGIG Sbjct: 182 LMGINVDTTISYTFAIGSALAAAAGVLVGLYYNTINPLMGVLPGLKAFIAAVFGGIGIIP 241 Query: 238 GAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281 GA+ GG +G+ + + + + YK VA L+I+IL I+P GL Sbjct: 242 GAMLGGFSLGIIETLVSGYGSSMYKDAVAFALLILILIIKPSGL 285 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: 201 Number of extensions: 13 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: 294 Length adjustment: 26 Effective length of query: 260 Effective length of database: 268 Effective search space: 69680 Effective search space used: 69680 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 24 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