Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_083774285.1 ADEG_RS07500 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_000024605.1:WP_083774285.1 Length = 159 Score = 119 bits (298), Expect = 4e-32 Identities = 55/133 (41%), Positives = 89/133 (66%), Gaps = 5/133 (3%) Query: 156 LHYLLQNTKIGKAMRAVADDLDLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVR 215 LH TK+G A+RA+A + DLA+VSGI++E+VI +TW + + + G T + Sbjct: 24 LHLFFTRTKVGLAIRAIATNPDLARVSGINLERVILFTWFLGAALAGVAGVFRAADTQLY 83 Query: 216 PNMGWFLILPLFASVILGGIGNPYGAIAAAFIIGIVQEVSTPF-----LGSQYKQGVALL 270 P MGW ++LP+FA+V+LGGIG+ YG I A++++G+ + + F L ++Y+ +A L Sbjct: 84 PMMGWDILLPVFAAVVLGGIGSFYGLIIASYLLGLAENLGVVFLQAVGLSTEYRMAIAFL 143 Query: 271 IMILVLLIRPKGL 283 ++ILVL+ RP+GL Sbjct: 144 VLILVLIFRPRGL 156 Lambda K H 0.328 0.144 0.426 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: 134 Number of extensions: 8 Number of successful extensions: 2 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: 288 Length of database: 159 Length adjustment: 22 Effective length of query: 266 Effective length of database: 137 Effective search space: 36442 Effective search space used: 36442 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 (21.7 bits) S2: 45 (21.9 bits)
Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_083774284.1 ADEG_RS07495 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_000024605.1:WP_083774284.1 Length = 167 Score = 79.7 bits (195), Expect = 4e-20 Identities = 52/148 (35%), Positives = 82/148 (55%), Gaps = 2/148 (1%) Query: 6 IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFV-NTFGVNIWLS 64 +QL++N + GSI LA GLTLTYG+ R NFA+ + +TLG + + V N W Sbjct: 5 LQLLLNSLITGSIYLLAGTGLTLTYGLSRFPNFAYAELITLGGFAAYTVLQRSSGNFWAG 64 Query: 65 MIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYN 124 +++A + V LS +L++S + + RA L++ SIGL LR + IW Y Sbjct: 65 LLLAFLICGLVSTLSYRLVFSPLVNRRAPLIPLMVASIGLGYVLRYTMGEIWSWSAVGYP 124 Query: 125 LPITPALDIFGVKVPQNQLLVLALAVLS 152 L + A + G++V L ++A+A+LS Sbjct: 125 L-VWTAYNWGGLRVTSLWLYLIAVALLS 151 Lambda K H 0.328 0.144 0.426 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: 138 Number of extensions: 8 Number of successful extensions: 2 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: 288 Length of database: 167 Length adjustment: 22 Effective length of query: 266 Effective length of database: 145 Effective search space: 38570 Effective search space used: 38570 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 (21.7 bits) S2: 45 (21.9 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