Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate AZOBR_RS08655 AZOBR_RS08655 amino acid ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >FitnessBrowser__azobra:AZOBR_RS08655 Length = 340 Score = 397 bits (1020), Expect = e-115 Identities = 192/337 (56%), Positives = 252/337 (74%), Gaps = 3/337 (0%) Query: 8 LAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADFCR 67 LA AA V G AQAG TLDAV+ +GFVQCGV+ GLPGF PDS+G G+D D+CR Sbjct: 6 LAAAAAAVVFGAVTGAQAGPTLDAVKGRGFVQCGVNAGLPGFGNPDSSGNWTGLDVDYCR 65 Query: 68 AVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGFITYY 127 AVA A+F D KVKF+ L+A++RF A+QSGE+D+LSRN+T+T +RD +GL F +TYY Sbjct: 66 AVAVALFNDPNKVKFTPLSAQQRFPAIQSGEVDLLSRNTTVTLTRDTSVGLNFAP-VTYY 124 Query: 128 DGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESAK 187 DG GF+ N KLGVKSAKEL+GAT+C+QAGTTTELN++DYFR N + Y P+ +++DE Sbjct: 125 DGQGFMVNKKLGVKSAKELNGATVCVQAGTTTELNLADYFRTNNMSYNPVVIESNDEVNA 184 Query: 188 SLESGRCDVLTSDKSQLFAQRSKLAS-PKDYVVLPETISKEPLGPVVRNGDDEWLAIVRW 246 + +GRCDVLT+D S L R+ +A P D+++LPE ISKEPL P VR+GDD+W +V+W Sbjct: 185 AYFAGRCDVLTTDASGLAGTRAGVAPVPDDHIILPEIISKEPLAPAVRHGDDQWFDVVKW 244 Query: 247 TGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQVGN 306 T YA + AEE G+TSKNV+ E ++KNP++ R+LG GK L L + W I+K +GN Sbjct: 245 TVYATIQAEEMGITSKNVD-EFVNSKNPEIQRILGTSPGMGKALGLDEKWAYNIIKTMGN 303 Query: 307 YGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 YGE+FERN+G TPL+++RGLNALW GG+QYA P+R Sbjct: 304 YGEIFERNVGTKTPLKLERGLNALWTNGGLQYAMPIR 340 Lambda K H 0.315 0.133 0.383 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: 428 Number of extensions: 16 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: 343 Length of database: 340 Length adjustment: 29 Effective length of query: 314 Effective length of database: 311 Effective search space: 97654 Effective search space used: 97654 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 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