Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_4013 Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
Query= reanno::acidovorax_3H11:Ac3H11_796 (577 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4013 Length = 580 Score = 842 bits (2174), Expect = 0.0 Identities = 398/569 (69%), Positives = 460/569 (80%), Gaps = 8/569 (1%) Query: 7 AIAFAAAALAMGQAAWAGEAE--AKKWIDSEFQPSTLNKDQQMAEMKWFIDAAKKLQAKG 64 ++A A + AAWA E AKKWI SEF+PSTL + QQ+ E+KWFI A++ + Sbjct: 13 SLAAMLALSGLSAAAWADAYEDAAKKWIGSEFKPSTLTEAQQLEELKWFIKASEPFRGMS 72 Query: 65 VKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQSGKSIYDG 124 +K VVSETI THEYESKTLAKAF EITGIK+ HDL+QEGDVVEKLQT MQS K+IYDG Sbjct: 73 IK---VVSETIATHEYESKTLAKAFTEITGIKLTHDLLQEGDVVEKLQTQMQSDKNIYDG 129 Query: 125 WISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGKLYQLPDQ 184 W++DSDLIGTH+RYGK ++TD M GK +T+P +D+KD+IG FTT PDGK+YQLPDQ Sbjct: 130 WVNDSDLIGTHFRYGKTESITDLMANEGKAYTSPTLDIKDFIGISFTTAPDGKVYQLPDQ 189 Query: 185 QFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNIDGKPIYG 244 QFANLYWFRAD F+R D+K KFK KYGY+LGVP+NWSAYEDIA FF+ D+K IDGK IYG Sbjct: 190 QFANLYWFRADWFERADLKAKFKEKYGYELGVPVNWSAYEDIARFFSEDIKEIDGKRIYG 249 Query: 245 HMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGASVARGGA 304 HMDYGKKDPSLGWRFTDAW SMAG D G PNGLP+DEWGIRV D C PVG+SV RGG Sbjct: 250 HMDYGKKDPSLGWRFTDAWFSMAGAGDKGIPNGLPVDEWGIRVED--CHPVGSSVTRGGD 307 Query: 305 TNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFTADMTKPG 364 TN PAAVYA TKYVDWMKKYAP EA GMTF E+GPVP+QG IAQQIFWYTAFTADMTKPG Sbjct: 308 TNGPAAVYATTKYVDWMKKYAPPEAAGMTFSESGPVPSQGNIAQQIFWYTAFTADMTKPG 367 Query: 365 LPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWLYAQFVTA 424 LPV+NADGTPKWRMAP P GPYW++GM+ GYQD GSWTF K + AAWLYAQFVT+ Sbjct: 368 LPVMNADGTPKWRMAPSPKGPYWEEGMKLGYQDAGSWTFLKSTPEKQKLAAWLYAQFVTS 427 Query: 425 KTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTNVPDYPKL 484 KT SLKKT+VGLTPIRESDI S+AMTD+APKLGGLVEFYRSPARV W+PTGTNVPDYP+L Sbjct: 428 KTVSLKKTIVGLTPIRESDINSQAMTDLAPKLGGLVEFYRSPARVQWTPTGTNVPDYPRL 487 Query: 485 AQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGM-AHCAPKLNAKSDPNKWLS 543 AQLWW ++A+A +GEKTPQ A+D LA + D +M RLER+ + C PK+N + D W Sbjct: 488 AQLWWSHIAEAASGEKTPQQALDGLAKDQDAIMTRLERSKVQPTCGPKMNPERDAQYWFD 547 Query: 544 DKQAPWKKLANEKPKGETIAYGTLLQAWK 572 AP KLANEKPKGET++Y LL++W+ Sbjct: 548 QPGAPKAKLANEKPKGETVSYAELLKSWE 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: 1321 Number of extensions: 68 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