Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 205 bits (522), Expect = 1e-57 Identities = 108/236 (45%), Positives = 155/236 (65%), Gaps = 6/236 (2%) Query: 21 TQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERG 80 + L+ +D E+ D +F+ ILG SG GK+TL+ ++AGL +G VLL G PV+GPGA+RG Sbjct: 16 SSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEVLLRGKPVDGPGADRG 75 Query: 81 MVFQSYTLFPWLTIEQNIRFGLRERGMPEA---QQKERAAYFIAKVGLRGFEQHFPKQLS 137 +VFQSY+L PWLT+E NI + + MP+A ++K R A +I VGL + P +LS Sbjct: 76 VVFQSYSLMPWLTVEGNIALAV-DAVMPDASKAERKARVAKYIGMVGLSHAAERRPSELS 134 Query: 138 GGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDID 197 GGM+QR A+ARALA P ILL+DEP ALD TR +Q+ + IWE E+KTV+ +T+D+D Sbjct: 135 GGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEAIWEQEKKTVILITNDVD 194 Query: 198 EAIFMANRVAVFSARPG-RIKTELAVDLPHPR-HYTIKTSPEFMDLKARLTEEIRA 251 EA+ +A+R+ + PG V+LP PR + + P+F L+A +TE + A Sbjct: 195 EALLLADRIIPLNPGPGATFGPSFKVNLPRPRDRAAVNSDPDFKRLRAEVTEYLMA 250 Score = 180 bits (456), Expect = 7e-50 Identities = 99/247 (40%), Positives = 147/247 (59%), Gaps = 7/247 (2%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 V V +++ T KG T + D ++ +F++++G SGCGKST+L + AGL + G Sbjct: 293 VEFSRVKKIYPTPKGPLT-VVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEG 351 Query: 64 RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKER---AAYFI 120 V+LDG V G +R +VFQ+ +LFPWLT QN+ G+ +R P A ER +Y++ Sbjct: 352 GVILDGREVSEAGPDRAVVFQAPSLFPWLTALQNVALGV-DRVYPHASPAERLDIVSYYL 410 Query: 121 AKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLG 180 +VGL +S GM+QR IARA A PK+LL+DEPFG LD+ TR +QE+L+ Sbjct: 411 ERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLME 470 Query: 181 IWEAERKTVLFVTHDIDEAIFMANRVAVFSARP-GRIKTELAVDLPHPR-HYTIKTSPEF 238 +W R T + VTHD+DEAI +A++V + + P RI L VD+P PR + P + Sbjct: 471 VWTRTRVTAICVTHDVDEAILLADKVVMMTNGPNARIGKVLNVDIPRPRTRRALLEHPRY 530 Query: 239 MDLKARL 245 + +A + Sbjct: 531 YEYRAEV 537 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: 398 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 259 Length of database: 553 Length adjustment: 30 Effective length of query: 229 Effective length of database: 523 Effective search space: 119767 Effective search space used: 119767 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