Align Extracellular solute-binding protein, family 7 (characterized, see rationale)
to candidate GFF3305 HP15_3247 twin-arginine translocation pathway signal
Query= uniprot:Q48AL6 (362 letters) >FitnessBrowser__Marino:GFF3305 Length = 358 Score = 457 bits (1176), Expect = e-133 Identities = 214/351 (60%), Positives = 281/351 (80%), Gaps = 4/351 (1%) Query: 7 VKAALVVSLGLSSLGLSALAHADDDKKYRWKLAETWGPNFPIFGDATKNMAKMVKEMSNG 66 V +A V+++ + ALA + +LAETWGPNFPIFGD TK A+ V++MS+G Sbjct: 6 VLSAAVLAVATTFASSQALAQ----DTFTLRLAETWGPNFPIFGDTTKRFAETVEKMSDG 61 Query: 67 RLTIRIDSSNKHKSALGIFDFVKSGQYQMGHSASYYWKGKNFNTMFFTTVPFGMIASEQH 126 RL +RIDS+NKHK+ LG+FD VK+GQY MGHSASYYWKGK T+FFT++PFGMIA EQ+ Sbjct: 62 RLKVRIDSANKHKAPLGVFDMVKAGQYDMGHSASYYWKGKVPETLFFTSMPFGMIAMEQY 121 Query: 127 AWFYYGGGMELMKKVYDQYGIMSFPGGNTGNQMGGWFKKEINSVEDLKGLKMRIPGFAGE 186 AWFY+GGGMELM++VY+ + ++SFPGGNTG QMGGWF+KEINS++DLKGLKMRIPGFAGE Sbjct: 122 AWFYHGGGMELMQEVYEPHNMLSFPGGNTGVQMGGWFRKEINSIDDLKGLKMRIPGFAGE 181 Query: 187 VLAKLGAKPTNIPSGELYTALERNTIDALEWVGPSLDLRMGFHKIAPYYYTGWHEPGTEL 246 V A++G PTNI GELYTALERNTIDA+EWVGP+LDLR+GF +IA YYYTGWHEP TEL Sbjct: 182 VFAEVGVNPTNIAPGELYTALERNTIDAVEWVGPALDLRLGFQQIADYYYTGWHEPATEL 241 Query: 247 QFMVNQKAYNSLPKDLQKILTVAMKAAAYDMYSQSMHASGVNLASLKKDYPNVQMRSFPK 306 QF+VN++ ++ LP DLQ+I+ VAM+ A+YDM QS HA+ A++K++YPNVQ++ FP Sbjct: 242 QFLVNKRVWDKLPADLQEIMRVAMRTASYDMLVQSQHANAEAWANIKEEYPNVQIKQFPD 301 Query: 307 PVMEAIVQANDELLEEFAAKDPMTAEILKSLNDYKHQIRAWTNLSDRAYLD 357 V +A+ AN++LL+E A M A+I++S +Y + RA+T++S+RAYL+ Sbjct: 302 DVFDAMYAANEKLLDEAAEGSEMAAKIIESQQNYLEKSRAYTDISERAYLN 352 Lambda K H 0.318 0.133 0.402 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: 442 Number of extensions: 12 Number of successful extensions: 1 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: 362 Length of database: 358 Length adjustment: 29 Effective length of query: 333 Effective length of database: 329 Effective search space: 109557 Effective search space used: 109557 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: 41 (21.7 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