Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate SM_b20569 SM_b20569 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Smeli:SM_b20569 Length = 256 Score = 203 bits (517), Expect = 3e-57 Identities = 100/225 (44%), Positives = 151/225 (67%), Gaps = 1/225 (0%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 V+++ +S+ F+ G+ L+ ++ ++R + + I+G SG GK+TLLR++AGL+ A +G Sbjct: 12 VALRDLSKSFQI-NGRPLSVLRNLNLDIRSGECLAIVGASGSGKTTLLRVLAGLETADAG 70 Query: 64 RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKV 123 RVL+DG PV G G ER ++FQ L PWLT+ N+ FGL+ RG + ++RA ++I+ V Sbjct: 71 RVLIDGRPVAGVGRERAVIFQEPRLLPWLTVLGNVAFGLKVRGEDSGRAEQRARHYISLV 130 Query: 124 GLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWE 183 GL F+ +PKQLSGGM QR +ARAL P+ILL+DEP GALD T++ MQ+ L IW Sbjct: 131 GLADFQDAYPKQLSGGMAQRVGLARALTVKPEILLLDEPLGALDAMTKLTMQQELERIWR 190 Query: 184 AERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPR 228 E T++ VTHD++EAI++A+RV + + + +DLP PR Sbjct: 191 EENVTMVLVTHDLEEAIYLADRVLILPKQKDGAPRAIDIDLPRPR 235 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: 187 Number of extensions: 5 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: 259 Length of database: 256 Length adjustment: 24 Effective length of query: 235 Effective length of database: 232 Effective search space: 54520 Effective search space used: 54520 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