Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 3609156 Dshi_2544 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Dino:3609156 Length = 269 Score = 187 bits (474), Expect = 3e-52 Identities = 100/235 (42%), Positives = 139/235 (59%), Gaps = 2/235 (0%) Query: 6 IQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRV 65 + ++RV +T AL+ VD +R F +++G SGCGKSTLL+I+AGL + GRV Sbjct: 18 VYELTRVSKTYARNSVVALEDVDLTLRKGSFTSVIGSSGCGKSTLLKIMAGLIPPSKGRV 77 Query: 66 LLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQK--ERAAYFIAKV 123 +L G PV G + GM+FQ TLFPW T +NI + R A K ++A + V Sbjct: 78 ILQGEPVRGARRDIGMMFQQATLFPWKTAVENIVLPIEIRDGKAAANKAMDKAYELLEIV 137 Query: 124 GLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWE 183 GL+GFE +P +LSGGM QR +I R L +P +LL+DEPF ALD +R +M L I Sbjct: 138 GLKGFENVYPNELSGGMAQRASICRMLITEPAVLLLDEPFSALDELSRDMMNMELQRICR 197 Query: 184 AERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEF 238 + T VTH I EA+ +++ + V RPGRI + VDLP PR + T+P+F Sbjct: 198 EQNATAFLVTHSIQEAVILSDDIVVMKPRPGRIAEIVEVDLPRPRTLDMMTTPKF 252 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: 8 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