Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate HSERO_RS04870 HSERO_RS04870 ABC transporter substrate-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_796 (577 letters) >FitnessBrowser__HerbieS:HSERO_RS04870 Length = 582 Score = 955 bits (2469), Expect = 0.0 Identities = 451/576 (78%), Positives = 501/576 (86%), Gaps = 2/576 (0%) Query: 4 QFKAIAFAAAALAMGQA--AWAGEAEAKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQ 61 + K AAA + G A AWA A+KW+DSEFQPSTL++ QQ++EM+WFIDAA KL+ Sbjct: 7 KIKLTVLAAAMVMAGVAGNAWADIKAAEKWVDSEFQPSTLSRPQQVSEMQWFIDAAAKLK 66 Query: 62 AKGVKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKSI 121 AKGVKEI VVSET+ TH YESKTLAKAFEEITGIKV HD+IQEGDVVEK+QTS+QSGKSI Sbjct: 67 AKGVKEIHVVSETLDTHAYESKTLAKAFEEITGIKVIHDVIQEGDVVEKMQTSLQSGKSI 126 Query: 122 YDGWISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQL 181 YDGW++DSDLIGTHYR G+ + LTDYM G GKE+TNPG+DLKD+IGT FTT PDGKLYQL Sbjct: 127 YDGWVNDSDLIGTHYRNGQTVVLTDYMAGPGKEYTNPGLDLKDFIGTSFTTAPDGKLYQL 186 Query: 182 PDQQFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGKP 241 PDQQFANLYWFRAD F RKD+++KFKAKYGY+LGVP NWSAYEDIA FFTNDVK +DGK Sbjct: 187 PDQQFANLYWFRADWFARKDLQEKFKAKYGYELGVPQNWSAYEDIAAFFTNDVKELDGKK 246 Query: 242 IYGHMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVAR 301 IYGHMDYGKKDPSLGWRFTDAWLSMAG AD G PNGLP+DEWGIRVADDKCTPVGASVAR Sbjct: 247 IYGHMDYGKKDPSLGWRFTDAWLSMAGAADKGLPNGLPVDEWGIRVADDKCTPVGASVAR 306 Query: 302 GGATNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMT 361 GGATNSPAAVYALTKY+DWMKKYAP EA GMTF EAGPVPAQG IAQQIFWY+AFTA MT Sbjct: 307 GGATNSPAAVYALTKYLDWMKKYAPPEALGMTFSEAGPVPAQGHIAQQIFWYSAFTASMT 366 Query: 362 KPGLPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQF 421 K GLPVVNADG+PKWRMAPGP+GPYWK GMQNGYQDVGSWTF K ++ AAAWLYAQF Sbjct: 367 KQGLPVVNADGSPKWRMAPGPHGPYWKDGMQNGYQDVGSWTFLKSTPPDQMAAAWLYAQF 426 Query: 422 VTAKTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDY 481 T+KT SLKK++VG+T IR+SDI+S T A K GGL+EFYRSPARVAW+PTGTNVPDY Sbjct: 427 TTSKTVSLKKSIVGVTFIRDSDIRSDYFTKNAAKYGGLIEFYRSPARVAWTPTGTNVPDY 486 Query: 482 PKLAQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGMAHCAPKLNAKSDPNKW 541 PK+AQ+WWKN++ A++GEKTPQGAMD LADEMD +MARL+RAGM CAPKLN K DP W Sbjct: 487 PKMAQIWWKNISSAISGEKTPQGAMDNLADEMDGIMARLQRAGMKQCAPKLNPKKDPATW 546 Query: 542 LSDKQAPWKKLANEKPKGETIAYGTLLQAWKDGKTR 577 LSDK APW KLANEKPKGETI Y LLQAWKDG+ R Sbjct: 547 LSDKGAPWAKLANEKPKGETIPYDKLLQAWKDGRVR 582 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: 1448 Number of extensions: 84 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: 582 Length adjustment: 36 Effective length of query: 541 Effective length of database: 546 Effective search space: 295386 Effective search space used: 295386 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