Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2490 (367 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 146 bits (368), Expect = 2e-39 Identities = 83/212 (39%), Positives = 128/212 (60%), Gaps = 5/212 (2%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 M L++K + K + S+++ IDLE+ D EF+ +G SG GK+TL+ L+AGL + G + Sbjct: 1 MPILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEV 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120 L G+ V D +VFQ+Y+L P ++V N++ A+D D E K A I Sbjct: 61 LLRGKP---VDGPGADRGVVFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYI 117 Query: 121 --LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178 + L ER+P +LSGG RQRVA+ RA+ +P I L DEPLS LDA R +++ E+ Sbjct: 118 GMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEA 177 Query: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNSG 210 + ++ + T+I +T+D EA+ LAD+++ LN G Sbjct: 178 IWEQEKKTVILITNDVDEALLLADRIIPLNPG 209 Score = 140 bits (353), Expect = 8e-38 Identities = 79/212 (37%), Positives = 125/212 (58%), Gaps = 15/212 (7%) Query: 17 SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELDGRDITEVTPAKRD 76 +++ G DL+++ EF+ +G SGCGKST+L + AGL +VSEG + LDGR+++E P D Sbjct: 310 TVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGGVILDGREVSEAGP---D 366 Query: 77 LAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARILE-------LGPLLER 129 A+VFQ +L+P ++ +N++ GVD+ + +E I+ LG +++ Sbjct: 367 RAVVFQAPSLFPWLTALQNVAL-----GVDRVYPHASPAERLDIVSYYLERVGLGDSMDK 421 Query: 130 KPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQATMIY 189 K +S G RQRV I RA +PK+ L DEP LD+ R +++ L + + T I Sbjct: 422 KASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWTRTRVTAIC 481 Query: 190 VTHDQVEAMTLADKVVVLNSGRIEQVGSPLEL 221 VTHD EA+ LADKVV++ +G ++G L + Sbjct: 482 VTHDVDEAILLADKVVMMTNGPNARIGKVLNV 513 Lambda K H 0.319 0.136 0.384 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: 436 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: 367 Length of database: 553 Length adjustment: 33 Effective length of query: 334 Effective length of database: 520 Effective search space: 173680 Effective search space used: 173680 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