Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate RR42_RS13765 RR42_RS13765 ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_796 (577 letters) >FitnessBrowser__Cup4G11:RR42_RS13765 Length = 576 Score = 1007 bits (2604), Expect = 0.0 Identities = 475/577 (82%), Positives = 517/577 (89%), Gaps = 1/577 (0%) Query: 1 MKMQFKAIAFAAAALAMGQAAWAGEAEAKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKL 60 MK+ A+A AAALA G AAWAGEAEAKKW+DSEFQPS+L KD+Q+AEMKWF+DAA KL Sbjct: 1 MKLGMTALA-CAAALACGHAAWAGEAEAKKWVDSEFQPSSLAKDKQLAEMKWFMDAAAKL 59 Query: 61 QAKGVKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKS 120 +AKGV +ISVVSET+TTHEYESKTLAKAFEEITGIKV HD+IQEGDVVEKLQTSMQSGKS Sbjct: 60 KAKGVTQISVVSETLTTHEYESKTLAKAFEEITGIKVNHDIIQEGDVVEKLQTSMQSGKS 119 Query: 121 IYDGWISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQ 180 IYDGWISDSDLIGTHYRYG I+ L+DYM GAGKEWTNPG+D+KD+IGTKFTT PDGKLYQ Sbjct: 120 IYDGWISDSDLIGTHYRYGAILPLSDYMSGAGKEWTNPGLDVKDFIGTKFTTAPDGKLYQ 179 Query: 181 LPDQQFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGK 240 LPDQQFANLYWFRAD F RKD++DKFKAKYGYDLGVP NWSAYEDIA FF+NDVK +DGK Sbjct: 180 LPDQQFANLYWFRADWFARKDLQDKFKAKYGYDLGVPTNWSAYEDIANFFSNDVKELDGK 239 Query: 241 PIYGHMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVA 300 +YGHMDYGKKDPSLGWRFTDAWLSMAG AD G PNG+P+DEWGIRV DKCTP GASVA Sbjct: 240 KVYGHMDYGKKDPSLGWRFTDAWLSMAGAADKGLPNGMPVDEWGIRVGADKCTPEGASVA 299 Query: 301 RGGATNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADM 360 RGGA NSPAAVYALTKY+DWMKKYAP +A GMTF EAGPVPAQGQIAQQ+FWYTAFTADM Sbjct: 300 RGGAANSPAAVYALTKYIDWMKKYAPPQAMGMTFSEAGPVPAQGQIAQQVFWYTAFTADM 359 Query: 361 TKPGLPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQ 420 TK GLPVVNADG+PKWRMAP P GPYWKQGMQNGYQDVGSWTFFK+ D N+ AAAWLYAQ Sbjct: 360 TKKGLPVVNADGSPKWRMAPSPYGPYWKQGMQNGYQDVGSWTFFKNTDPNRLAAAWLYAQ 419 Query: 421 FVTAKTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPD 480 FVT+KT SLKK++ GLT IR+SDI + +T A + GGL+EFYRSPARVAW+PTGTNVPD Sbjct: 420 FVTSKTVSLKKSLTGLTFIRDSDIHHEYLTKNAAQYGGLIEFYRSPARVAWTPTGTNVPD 479 Query: 481 YPKLAQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGMAHCAPKLNAKSDPNK 540 YPKLAQLWWKNVA AVTGEKTPQ AMD LA+EMDQVM RL+RAGM +CAPKLN K DP K Sbjct: 480 YPKLAQLWWKNVATAVTGEKTPQAAMDNLAEEMDQVMGRLQRAGMTNCAPKLNPKGDPAK 539 Query: 541 WLSDKQAPWKKLANEKPKGETIAYGTLLQAWKDGKTR 577 WLSD APWKKLANEKPKGETIAY LLQAWK+GK R Sbjct: 540 WLSDDHAPWKKLANEKPKGETIAYDKLLQAWKEGKVR 576 Lambda K H 0.315 0.132 0.412 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: 1454 Number of extensions: 77 Number of successful extensions: 1 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: 577 Length of database: 576 Length adjustment: 36 Effective length of query: 541 Effective length of database: 540 Effective search space: 292140 Effective search space used: 292140 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: 53 (25.0 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