Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF1035 HP15_1014 nitrate ABC transporter, ATPase subunits C and D
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Marino:GFF1035 Length = 302 Score = 205 bits (521), Expect = 1e-57 Identities = 105/241 (43%), Positives = 157/241 (65%), Gaps = 4/241 (1%) Query: 2 SSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHAT 61 S + + +S+V+ +G + + F + +FV I+G SGCGKST+L ++AGLD A+ Sbjct: 4 SFLEVDGLSKVYPDGQGGELTVFEDIRFALEKGEFVCIIGHSGCGKSTILNVLAGLDEAS 63 Query: 62 SGRVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQK--ERAAYF 119 +G V+++G ++GPG ERG+VFQ+Y+L PW T NI F +R R +++K E + + Sbjct: 64 AGNVVMNGKEIKGPGLERGVVFQNYSLLPWKTTLNNIVFAVRARWPEWSKEKVKEHSERY 123 Query: 120 IAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLL 179 + VGL P QLSGGM+QR +IARA A P++LL+DEPFGALD TR ++Q+ L+ Sbjct: 124 LKMVGLDHALNRKPSQLSGGMRQRVSIARAFATQPELLLLDEPFGALDALTRGVIQDELV 183 Query: 180 GIWEAERKTVLFVTHDIDEAIFMANRVAVFSARP-GRIKTELAVDLPHPR-HYTIKTSPE 237 IWE R+TV +THD+DEAI +++R+ + S P RI + VD+PHPR TI +P Sbjct: 184 KIWEETRQTVFMITHDVDEAILLSDRIFLMSNGPNARIAESVKVDIPHPRARATIFQNPA 243 Query: 238 F 238 + Sbjct: 244 Y 244 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: 209 Number of extensions: 10 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: 259 Length of database: 302 Length adjustment: 26 Effective length of query: 233 Effective length of database: 276 Effective search space: 64308 Effective search space used: 64308 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