Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate Pf6N2E2_108 Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
Query= reanno::acidovorax_3H11:Ac3H11_796 (577 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_108 Length = 580 Score = 845 bits (2182), Expect = 0.0 Identities = 402/569 (70%), Positives = 466/569 (81%), Gaps = 8/569 (1%) Query: 7 AIAFAAAALAMGQAAWAGEAE--AKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQAKG 64 ++A A + AAWA E AKKWI SEF+PSTL +QQ+ E+KWFI AA+ +G Sbjct: 13 SLAAMLALSGLSAAAWADAYEDAAKKWIGSEFKPSTLTAEQQLEELKWFIKAAQPF--RG 70 Query: 65 VKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKSIYDG 124 +K I+VVSETI THEYESK LAKAF EITGI++ HDL+QEGDVVEKLQT MQS K+IYDG Sbjct: 71 MK-INVVSETIATHEYESKVLAKAFSEITGIQLTHDLLQEGDVVEKLQTQMQSDKNIYDG 129 Query: 125 WISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQLPDQ 184 W++DSDLIGTH+RYGK ++TD M GK++T+P +DLKD+IG FTT PDGK+YQLPDQ Sbjct: 130 WVNDSDLIGTHFRYGKTESITDLMANEGKDFTSPTLDLKDFIGISFTTAPDGKVYQLPDQ 189 Query: 185 QFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGKPIYG 244 QFANLYWFRAD F+R D+K KFK KYGY+LGVP+NWSAYEDIA+FF+ DVK IDGK +YG Sbjct: 190 QFANLYWFRADWFERADLKAKFKEKYGYELGVPVNWSAYEDIAKFFSEDVKEIDGKRVYG 249 Query: 245 HMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVARGGA 304 HMDYGKKDPSLGWRFTDAW SMAG D G PNGLP+DEWGIRV D C PVG+SV RGG Sbjct: 250 HMDYGKKDPSLGWRFTDAWFSMAGGGDKGLPNGLPVDEWGIRVED--CHPVGSSVTRGGD 307 Query: 305 TNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMTKPG 364 TN PAAV+A TKYVDWMKKYAP EA GMTF E+GPVP+QG IAQQIFWYTAFTADMTKPG Sbjct: 308 TNGPAAVFATTKYVDWMKKYAPPEAAGMTFSESGPVPSQGNIAQQIFWYTAFTADMTKPG 367 Query: 365 LPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQFVTA 424 LPVVNADGTPKWRMAP P GPYW++GM+ GYQDVGSWTF K + AAWLYAQFVT+ Sbjct: 368 LPVVNADGTPKWRMAPSPRGPYWEEGMKLGYQDVGSWTFMKSTPEKQKLAAWLYAQFVTS 427 Query: 425 KTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDYPKL 484 KT SLKKT+VGLTPIRESDI S+A+TD+APKLGGLVEFYRSPARV W+PTGTNVPDYP+L Sbjct: 428 KTVSLKKTIVGLTPIRESDINSQALTDLAPKLGGLVEFYRSPARVQWTPTGTNVPDYPRL 487 Query: 485 AQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERA-GMAHCAPKLNAKSDPNKWLS 543 AQLWW ++A+A +GEKTPQ A+D LA + D +M RLER+ A CAPK+N + D W Sbjct: 488 AQLWWSHIAEAASGEKTPQQALDGLAKDQDAIMTRLERSKAQATCAPKMNPERDAQYWFD 547 Query: 544 DKQAPWKKLANEKPKGETIAYGTLLQAWK 572 AP KLANEKPKGET++Y LL++W+ Sbjct: 548 QPGAPKPKLANEKPKGETVSYTELLKSWE 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: 1320 Number of extensions: 67 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: 577 Length of database: 580 Length adjustment: 36 Effective length of query: 541 Effective length of database: 544 Effective search space: 294304 Effective search space used: 294304 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