Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 3610800 Dshi_4186 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Dino:3610800 Length = 273 Score = 223 bits (569), Expect = 2e-63 Identities = 114/252 (45%), Positives = 162/252 (64%), Gaps = 4/252 (1%) Query: 3 SVSIQAVSRVF---ETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDH 59 ++ ++ + + F E Q+ AL +D +R +F+TI+GPSGCGK+TLL+I+A L Sbjct: 10 AIELRGIRKTFTLSEDRDAQKVLALDGIDLTIRQGEFLTIIGPSGCGKTTLLKIIASLIS 69 Query: 60 ATSGRVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYF 119 G V+++G PV P R MVFQ++ LFPW T+ N+ F L R A+ +E A Sbjct: 70 HDEGDVVVEGKPVHEPDISRAMVFQTFGLFPWKTVIDNVTFPLTVRNFAPAEAREIAMKH 129 Query: 120 IAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLL 179 I +VGL F +P QLSGGMQQR +ARAL+ ILLMDEPFGA+D QTR LMQE L+ Sbjct: 130 IEQVGLGKFVDAYPHQLSGGMQQRVGLARALSTGADILLMDEPFGAIDAQTRELMQEELM 189 Query: 180 GIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPR-HYTIKTSPEF 238 I + E+KTV+F+THD+DEA+ +A+RV + S PGR++ + VDLP PR Y ++ F Sbjct: 190 RICQREQKTVVFITHDLDEAVLLADRVLLMSRGPGRVREVIDVDLPRPRFDYDVRGHASF 249 Query: 239 MDLKARLTEEIR 250 + ++ L E+R Sbjct: 250 IKVRGHLWHELR 261 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: 213 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: 273 Length adjustment: 25 Effective length of query: 234 Effective length of database: 248 Effective search space: 58032 Effective search space used: 58032 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