Align Inositol ABC transporter, periplasmic inositol-binding protein IbpA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate HSERO_RS05315 HSERO_RS05315 LacI family transcriptional regulator
Query= TCDB::B8H228 (326 letters) >FitnessBrowser__HerbieS:HSERO_RS05315 Length = 302 Score = 114 bits (285), Expect = 3e-30 Identities = 93/305 (30%), Positives = 148/305 (48%), Gaps = 21/305 (6%) Query: 18 LGLGTAALGLMTGCARGGAEAEVVVSFNDLSQPFFVAMRRELEDEAAKLGVKVQVLDAQN 77 + L L A+ ++ ++ +SF +++ P+FV+M++ L++ A LG KV DA + Sbjct: 6 IALALTTLAAAPAMAQEVSKLKIGMSFQEMNNPYFVSMKKALDEAAKSLGAKVIATDAAH 65 Query: 78 NSSKQISDLQAAAVQGAKVVIVAPTDSKALAGAADDLVEQGVAVISVDRNIAGGKTAVPH 137 N +KQI+D++ Q ++++ PTDS + A + V V++VD N +G Sbjct: 66 NVAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDANASG--PVDMF 123 Query: 138 VGADNVAGG----RAMADWVVKTYPAGARVVVITNDPGSSSSIERVKGVHDGLAAGGPAF 193 VG+ N G RA+AD + G V I + ++RV+G LA Sbjct: 124 VGSKNKDAGYQSCRALADAI-----GGKGEVAILDGIPVVPILQRVEGCKQALAE-YKDI 177 Query: 194 KIVTEQTANSKRDQALTVTQNILTSMRDTPPDVILCLNDDMAMGALEAVRAAGLDSAKVK 253 K+V Q R AL V +N++ S + I +ND AMGAL A++ +G D +K Sbjct: 178 KLVATQNGRQDRSVALGVVENMIQSRPNLKG--IFSVNDGGAMGALAAIQGSGKD---IK 232 Query: 254 VIGFDAIPEALARI-KAGEMVATVEQNPGLQIRTALRQAVDKIKSGAAL--KSVSLKPVL 310 + D PEA+ I G V T Q P Q+R L A+ K K GA + K V + + Sbjct: 233 LTSVDGAPEAVKAIADGGPFVETTAQFPRDQVRVGLAMALAK-KWGARVVPKEVPIDVMP 291 Query: 311 ITSGN 315 +T N Sbjct: 292 VTKKN 296 Lambda K H 0.315 0.130 0.353 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: 226 Number of extensions: 14 Number of successful extensions: 3 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: 326 Length of database: 302 Length adjustment: 27 Effective length of query: 299 Effective length of database: 275 Effective search space: 82225 Effective search space used: 82225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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