Align GlpV, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF511 PGA1_c05230 ABC transporter, extracellular solute-binding protein
Query= TCDB::G3LHZ3 (569 letters) >FitnessBrowser__Phaeo:GFF511 Length = 577 Score = 711 bits (1835), Expect = 0.0 Identities = 352/575 (61%), Positives = 428/575 (74%), Gaps = 19/575 (3%) Query: 4 TAGLLLAMTA--SAYAGMDEAKTFLDKEVGDLSTLPRADQEKEMQWFVDAAKPFAGMDIK 61 +A ++A+ A +AYA AK ++D+E S L + +Q EMQWF+ A++PF+GM+I Sbjct: 7 SAAAVIAVVAGQAAYADEAAAKKWIDEEFQP-SVLTKDEQLSEMQWFIKASEPFSGMEIN 65 Query: 62 VVSETITTHEYESKVLAPAFTAITGIKITHDLIGEGDVVEKLQTQMQSGENIYDAYINDS 121 V+SE I TH YES+VL AF ITGIK+ H ++GEG+VV+ +QTQMQ+ N+YDAY+NDS Sbjct: 66 VLSEGIPTHSYESEVLTKAFEEITGIKVNHQILGEGEVVQAVQTQMQTKRNLYDAYVNDS 125 Query: 122 DLIGTHWRYQQARSLTDWMANEGKDVTNPGLDIDDFIGKSFTTAPDGKLYQLPDQQFANL 181 DLIGTH R Q A +LTD M + DVTNP LD+ DF+G FTT PDG LYQLPDQQFANL Sbjct: 126 DLIGTHSRLQLAYNLTDMMEGDFFDVTNPELDLGDFMGTQFTTGPDGDLYQLPDQQFANL 185 Query: 182 YWFRYDWFNDEKNKADFKAKYGYDLGVPVNWSAYEDIAEFFTG--REIDGKKVFGHMDYG 239 YWFR DWF+ E +A FK KYGYDLGVPVNWSAYEDIAEFF+ +EIDG +FGHMDYG Sbjct: 186 YWFRKDWFDREDLQAAFKEKYGYDLGVPVNWSAYEDIAEFFSNDVKEIDGTTIFGHMDYG 245 Query: 240 KKDPSLGWRFTDAWLSMAGNGDKGIPNGKPVDEWGIKVDENS-RPVGSCVARGGDTNGPA 298 K+ P LGWR TDAWLSMAG G KG PNG P+DEWGI+++ +S P G+ V RGG NGPA Sbjct: 246 KRAPDLGWRMTDAWLSMAGAGSKGEPNGVPIDEWGIRMEADSCNPAGASVTRGGAANGPA 305 Query: 299 AVYSIQKYLDWMKAYAPAAAQGMTFSESGPVPSQGEVAQQMFTYTAFTADFVK---EGLP 355 AVY+I+K+ +W++ +AP A F +S P +QG VAQQ+F YTAFTAD VK EG Sbjct: 306 AVYAIRKWDEWLRKFAPPGAASYDFYQSLPALAQGNVAQQIFWYTAFTADMVKPQSEGNN 365 Query: 356 VVNADGTPKWRFAPSPHGVYWKDGMKLGYQDAGSWTLMKSTPDDRAKAAWLYAQFVTSKT 415 V+ +G P WR APSPHG YW++G K+GYQD GSWT +KSTP DRAKAAWLYAQFV SKT Sbjct: 366 TVDGEGNPLWRMAPSPHGPYWEEGQKVGYQDVGSWTFLKSTPMDRAKAAWLYAQFVVSKT 425 Query: 416 VDVKKSHMGLTFIRQSTLDHKSFTDRAPKLGGLIEFYRSPARLQWSPTGTNVPDYPKLAQ 475 VDVKKSH+GLTFIR S+++H+SFT+RAPKLGGL+EFYRSP R+ WSPTG NVPDYPKLAQ Sbjct: 426 VDVKKSHVGLTFIRDSSVNHESFTERAPKLGGLVEFYRSPDRVAWSPTGVNVPDYPKLAQ 485 Query: 476 LWWQAIGDASSGAKTAQEAMDSLCSEQEKVLQRLER----AKVQGDIGPKLAEEHDLAYW 531 +WWQ IGD +SGA T QEAMD L E + + R++R A V G GP+L EE D +W Sbjct: 486 IWWQQIGDVNSGAFTPQEAMDRLAEEMDITMARMQRADEQASVYGGCGPRLNEEKDAEWW 545 Query: 532 NADAVKNGNLAPQLKIENEKDKPVTVNYDELVKSW 566 A NG P K+ENEK + TVNYDELV W Sbjct: 546 YA----NGGAKP--KLENEKPQGQTVNYDELVARW 574 Lambda K H 0.315 0.132 0.409 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: 1285 Number of extensions: 57 Number of successful extensions: 6 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: 569 Length of database: 577 Length adjustment: 36 Effective length of query: 533 Effective length of database: 541 Effective search space: 288353 Effective search space used: 288353 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 (21.5 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