Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 3607975 Dshi_1383 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Dino:3607975 Length = 269 Score = 187 bits (476), Expect = 1e-52 Identities = 97/216 (44%), Positives = 135/216 (62%), Gaps = 3/216 (1%) Query: 23 ALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERGMV 82 AL+ + + DF+++LGPSGCGKST LRI+A L H T G V G G + G+V Sbjct: 38 ALRDLSLTINQGDFMSLLGPSGCGKSTALRIIADLLHPTRGSVDWTGQHDTG---DLGVV 94 Query: 83 FQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSGGMQQ 142 FQ TL PW T+ QN R RG P K+ + VGL F+ +P++LSGGM+ Sbjct: 95 FQEPTLMPWATVAQNTYLPYRLRGKPYNAVKDEVLEALKLVGLEKFQNAYPRELSGGMKM 154 Query: 143 RTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDEAIFM 202 R +IARA+ P+++LMDEPF ALD TR + LL + E TV+FVTH + E++F+ Sbjct: 155 RVSIARAMVTRPRLILMDEPFAALDEITRFKLNNDLLALKEKIGCTVIFVTHSVFESVFL 214 Query: 203 ANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEF 238 ++R+ V +ARPGR+ E+ VD P+PR T +TSPE+ Sbjct: 215 SDRIVVMAARPGRVLREVQVDAPYPRTETFRTSPEY 250 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: 163 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: 269 Length adjustment: 25 Effective length of query: 234 Effective length of database: 244 Effective search space: 57096 Effective search space used: 57096 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