Align glucose transporter, permease component (characterized)
to candidate 3608606 Dshi_1999 inner-membrane translocator (RefSeq)
Query= reanno::Phaeo:GFF3640 (433 letters) >FitnessBrowser__Dino:3608606 Length = 435 Score = 632 bits (1631), Expect = 0.0 Identities = 315/428 (73%), Positives = 363/428 (84%) Query: 5 TSQPIPEHSKRGLFQQLELDVRLLGMIGAFVILCIGFNILTDGRFLTPRNIFNLTIQTVS 64 T +P +KR Q LELD RLLGMIGAFV++C+ FN+LTDGRFLT RNIFNL+IQTVS Sbjct: 7 TESRLPSRAKRSFLQTLELDTRLLGMIGAFVLVCLVFNLLTDGRFLTARNIFNLSIQTVS 66 Query: 65 VAIMATGMVFVIVTRHIDLSVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAV 124 VAIMATGMVF+IVTRHIDL+VGALLATCSA MA+ QT +LP +FGL L HPA I + V Sbjct: 67 VAIMATGMVFIIVTRHIDLAVGALLATCSAAMAMTQTAILPQVFGLELGHPAIPWIAMLV 126 Query: 125 GLAIGTLIGAFQGWMVGFLTIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTFLVFGGT 184 GL GT+IGAFQG++VG+L IPAFIVTLGG LVWRNVAWY+T+GQTIGPLD TF+ GG Sbjct: 127 GLVTGTVIGAFQGYLVGYLMIPAFIVTLGGLLVWRNVAWYMTNGQTIGPLDPTFMTLGGI 186 Query: 185 SGTLGTTLSWVVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVA 244 +GTLG TLSW+VG+VA + A ALW+ R+ K H PVKP WAE + G ++ +ILGFVA Sbjct: 187 NGTLGATLSWIVGLVAVVAACWALWSGRKNKIAHDAPVKPVWAELTVMGVVSVAILGFVA 246 Query: 245 ILNAYQIPARRLKRMMEAQGETMPEGLVVGYGLPISVLILIATAVVMTIIARRTRLGRYI 304 ILN+Y++P RL+R+ EA+GE MPEG YG+P SVL+LIA AV MT+IA++TR GRYI Sbjct: 247 ILNSYEVPTARLRRLFEARGEVMPEGYTEVYGIPYSVLLLIAVAVAMTVIAKKTRFGRYI 306 Query: 305 FATGGNPDAAELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIA 364 FATGGNPDAAELSGINTR+LTVK+FALMG LCA+SA+VASARL NHSNDIGTLDELRVIA Sbjct: 307 FATGGNPDAAELSGINTRMLTVKVFALMGALCAISAIVASARLTNHSNDIGTLDELRVIA 366 Query: 365 AAVIGGTALSGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDIL 424 AAVIGGTAL+GG GTIYGAILGALIMQSLQSGMAMVGVDAP QNIVVGTVLVAAV IDIL Sbjct: 367 AAVIGGTALAGGIGTIYGAILGALIMQSLQSGMAMVGVDAPLQNIVVGTVLVAAVLIDIL 426 Query: 425 YRKRVGAR 432 YRKR+GA+ Sbjct: 427 YRKRMGAK 434 Lambda K H 0.327 0.141 0.419 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: 795 Number of extensions: 40 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: 433 Length of database: 435 Length adjustment: 32 Effective length of query: 401 Effective length of database: 403 Effective search space: 161603 Effective search space used: 161603 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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