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 BPHYT_RS16065 BPHYT_RS16065 LacI family transcriptional regulator
Query= TCDB::B8H228 (326 letters) >FitnessBrowser__BFirm:BPHYT_RS16065 Length = 317 Score = 129 bits (324), Expect = 1e-34 Identities = 92/300 (30%), Positives = 151/300 (50%), Gaps = 13/300 (4%) Query: 20 LGTAALGL--MTGCARGGAEAEVVVSFNDLSQPFFVAMRRELEDEAAKLGVKVQVLDAQN 77 L T A GL + A A ++ ++F +L+ P+FV M++ L D AA +G V V DA + Sbjct: 21 LATLAFGLSFIAAPAAQAAPLKIGMTFQELNNPYFVTMQKALNDAAASIGATVVVTDAHH 80 Query: 78 NSSKQISDLQAAAVQGAKVVIVAPTDSKALAGAADDLVEQGVAVISVDRNIAGGKTAVPH 137 + SKQ+SD++ + +++V PTDS + A + GV V++VD N G + Sbjct: 81 DVSKQVSDVEDMLQKKIDILLVNPTDSTGIQSAVTSAKKAGVVVVAVDANANGPVDS--F 138 Query: 138 VGADNVAGGRAMADWVVKTYPAGARVVVITNDPGSSSSIERVKGVHDGLAAGGPAFKIVT 197 VG+ N G +++ K+ V ++ P +ERV+G LA P K+V Sbjct: 139 VGSKNYDAGEMACEYLAKSIGGSGEVAILDGIP-VVPILERVRGCKAALAK-APGVKLVD 196 Query: 198 EQTANSKRDQALTVTQNILTSMRDTPPDVILCLNDDMAMGALEAVRAAGLDSAKVKVIGF 257 Q +R AL+VT+N++ + + + +ND +MGAL A+ ++G D +K+ Sbjct: 197 TQNGKQERATALSVTENMIQAHPNLKG--VFSVNDGGSMGALSAIESSGKD---IKLTSV 251 Query: 258 DAIPEALARIKA--GEMVATVEQNPGLQIRTALRQAVDKIKSGAALKSVSLKPVLITSGN 315 D PEA+A I+ + V T Q P Q+R AL A+ K K++ + +I N Sbjct: 252 DGAPEAIAAIQKPNSKFVETSAQFPADQVRIALGIALAKKWGANVPKTIPVDVKMIDKSN 311 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: 222 Number of extensions: 8 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: 317 Length adjustment: 28 Effective length of query: 298 Effective length of database: 289 Effective search space: 86122 Effective search space used: 86122 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