Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 153 bits (387), Expect = 9e-42 Identities = 83/212 (39%), Positives = 130/212 (61%), Gaps = 5/212 (2%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M LE++ + K YG L+ ID+ +E GEF+ +LG SG GK+TL++++AGL +P G++ Sbjct: 1 MPILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEV 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLE--MRRVPQAEHDKAVRDTA 118 L+ + V G D +VFQSY+L P L+V NI ++ M +AE V Sbjct: 61 LLRGKPVDG---PGADRGVVFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYI 117 Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 ++ + + +R+PS+LSGG RQRVA+ RAL +P + L DEPLS LDA R +++ E++ Sbjct: 118 GMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEA 177 Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDG 210 + + + TV+ +T+D EA+ LA RI + G Sbjct: 178 IWEQEKKTVILITNDVDEALLLADRIIPLNPG 209 Score = 128 bits (321), Expect = 4e-34 Identities = 76/214 (35%), Positives = 120/214 (56%), Gaps = 11/214 (5%) Query: 4 LEIRNIRKRY----GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59 +E ++K Y G + + G D+ + GEF+ L+G SGCGKST+L + AGL + S G Sbjct: 293 VEFSRVKKIYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGG 352 Query: 60 ILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTAR 119 +++ R V P D A+VFQ+ +L+P L+ +N+ G++ R P A + + + Sbjct: 353 VILDGREVSEAGP---DRAVVFQAPSLFPWLTALQNVALGVD-RVYPHASPAERLDIVSY 408 Query: 120 LLQIENL---LDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTEL 176 L+ L +D+K S +S G RQRV I RA +P++ L DEP LD+ R E++ L Sbjct: 409 YLERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVL 468 Query: 177 KRLHQMLRTTVVYVTHDQIEAMTLATRIAVMRDG 210 + R T + VTHD EA+ LA ++ +M +G Sbjct: 469 MEVWTRTRVTAICVTHDVDEAILLADKVVMMTNG 502 Lambda K H 0.320 0.136 0.385 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: 453 Number of extensions: 23 Number of successful extensions: 6 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: 360 Length of database: 553 Length adjustment: 32 Effective length of query: 328 Effective length of database: 521 Effective search space: 170888 Effective search space used: 170888 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 (21.8 bits) S2: 51 (24.3 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