Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate CCNA_00902 CCNA_00902 inositol ABC transporter, periplasmic inositol-binding protein IbpA
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__Caulo:CCNA_00902 Length = 326 Score = 157 bits (396), Expect = 4e-43 Identities = 99/308 (32%), Positives = 169/308 (54%), Gaps = 17/308 (5%) Query: 1 MNMKKLATLVSAVALSA------TVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADK 54 M+ ++L L + + L T A A+ + + + L+ PFFV+++ + EA K Sbjct: 6 MSRRRLLGLAAGLGLGTAALGLMTGCARGGAEAEVVVSFNDLSQPFFVAMRRELEDEAAK 65 Query: 55 LGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLD 114 LG + VLD+QNN +K+++++Q V+G K++++ PTDS A+ A + + VI++D Sbjct: 66 LGVKVQVLDAQNNSSKQISDLQAAAVQGAKVVIVAPTDSKALAGAADDLVEQGVAVISVD 125 Query: 115 RQATKGE-VVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQA 173 R G+ V H+ +DNV GG+ D++ K GA+V+ + G+S++ ER +G Sbjct: 126 RNIAGGKTAVPHVGADNVAGGRAMADWVVKTYPAGARVVVITNDPGSSSSIERVKGVHDG 185 Query: 174 VAA--HKFNVLASQPADFDRIKGLNVMQNLLTAHPDV--QAVFAQNDEMALGALRALQTA 229 +AA F ++ Q A+ R + L V QN+LT+ D + ND+MA+GAL A++ A Sbjct: 186 LAAGGPAFKIVTEQTANSKRDQALTVTQNILTSMRDTPPDVILCLNDDMAMGALEAVRAA 245 Query: 230 G--KSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPD-QIGAKGVETADKVLKGEKVQAKY 286 G + V V+GFD P+ + G++ AT+ Q P QI + DK+ G +++ Sbjct: 246 GLDSAKVKVIGFDAIPEALARIKAGEMVATVEQNPGLQIRTALRQAVDKIKSGAALKS-- 303 Query: 287 PVDLKLVV 294 V LK V+ Sbjct: 304 -VSLKPVL 310 Lambda K H 0.313 0.129 0.344 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: 228 Number of extensions: 13 Number of successful extensions: 4 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: 296 Length of database: 326 Length adjustment: 27 Effective length of query: 269 Effective length of database: 299 Effective search space: 80431 Effective search space used: 80431 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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