Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Synpcc7942_1237 Synpcc7942_1237 nitrate transport ATP-binding subunits C and D
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__SynE:Synpcc7942_1237 Length = 659 Score = 183 bits (464), Expect = 9e-51 Identities = 102/257 (39%), Positives = 156/257 (60%), Gaps = 6/257 (2%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 +++ V +VF+ G + AL+ V +R +F++++G SGCGKSTLL ++AGL +SG Sbjct: 5 LAVDHVHQVFDLPGGGQYIALKDVSLNIRPGEFISLIGHSGCGKSTLLNLIAGLAQPSSG 64 Query: 64 RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYF---I 120 ++L+G V PG +R +VFQ+Y+L PW T+ QNI + + + + + ER I Sbjct: 65 GIILEGRQVTEPGPDRMVVFQNYSLLPWRTVRQNIALAV-DSVLHDRNRTERRTIIEETI 123 Query: 121 AKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLG 180 VGLR +P ++SGGM+QR AIAR LA PK+LL+DEPFGALD TR +QE L+ Sbjct: 124 DLVGLRAAADKYPHEISGGMKQRVAIARGLAIRPKLLLLDEPFGALDALTRGNLQEQLMR 183 Query: 181 IWEAERKTVLFVTHDIDEAIFMANRVAVFSARP-GRIKTELAVDLPHPR-HYTIKTSPEF 238 I + T + VTHD+DEA+ +++RV + + P +I L VD P PR + +P + Sbjct: 184 ICQEAGVTAVMVTHDVDEALLLSDRVVMLTNGPAAQIGQILEVDFPRPRQRLEMMETPHY 243 Query: 239 MDLKARLTEEIRAESMA 255 DL+ L ++ + A Sbjct: 244 YDLRNELINFLQQQRRA 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: 414 Number of extensions: 24 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: 659 Length adjustment: 31 Effective length of query: 228 Effective length of database: 628 Effective search space: 143184 Effective search space used: 143184 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: 50 (23.9 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