Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF1363 Psest_1398 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__psRCH2:GFF1363 Length = 267 Score = 228 bits (581), Expect = 1e-64 Identities = 120/248 (48%), Positives = 159/248 (64%), Gaps = 1/248 (0%) Query: 3 SVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATS 62 ++S VS+VF ++ G AL F++ ++F+ +LGPSGCGKSTLLRI+AGL T Sbjct: 13 NISFDRVSQVFTSSDGSEVVALDNASFDIGRHEFIAVLGPSGCGKSTLLRILAGLVRPTH 72 Query: 63 GRVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRER-GMPEAQQKERAAYFIA 121 G+V + G+PV+GP E G+VFQ TL PWL I N+ F +R + G AQ+ R + Sbjct: 73 GQVSIYGSPVDGPRDEIGIVFQRPTLLPWLNIRDNLTFPMRHKYGRVTAQEITRGEELLE 132 Query: 122 KVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGI 181 VGL+ F P +LSGGMQQR AIARAL +DP+ILLMDEPF ALD TR + LL I Sbjct: 133 LVGLKEFGNKRPDELSGGMQQRAAIARALLHDPEILLMDEPFSALDALTRDELSLELLNI 192 Query: 182 WEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDL 241 W KTVLF+TH I EA+ +A+R+ V SARPGR++ + VDLP PR T P F +L Sbjct: 193 WTQRPKTVLFITHSIPEALLLADRILVMSARPGRVQEIIDVDLPRPRSMETLTEPRFNEL 252 Query: 242 KARLTEEI 249 + ++ Sbjct: 253 ANHIRRKV 260 Lambda K H 0.322 0.136 0.394 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: 211 Number of extensions: 7 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: 259 Length of database: 267 Length adjustment: 25 Effective length of query: 234 Effective length of database: 242 Effective search space: 56628 Effective search space used: 56628 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 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