Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SM_b20894 SM_b20894 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Smeli:SM_b20894 Length = 506 Score = 750 bits (1937), Expect = 0.0 Identities = 378/476 (79%), Positives = 426/476 (89%) Query: 36 LVGENGAGKSTLMKVLSGVYPAGTYEGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVP 95 L G+ KSTLMKVLSGVYPAGTYEGEIHY+G +R F I+DSE++GIIIIHQELALVP Sbjct: 31 LSGKTAPAKSTLMKVLSGVYPAGTYEGEIHYDGELRQFSTISDSEELGIIIIHQELALVP 90 Query: 96 LLSIAENIFLGNEVASNGVISWQQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIA 155 LLSIAENIFLGNEVA GVI W QTF RT+ELLKKVGL ESP TLITDIGVGKQQLVEIA Sbjct: 91 LLSIAENIFLGNEVAEKGVIHWPQTFARTQELLKKVGLNESPATLITDIGVGKQQLVEIA 150 Query: 156 KALSKSVKLLILDEPTASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITV 215 KALSK V+LLILDEPTASLNE+DS+ALL LLMEFR+QGMTSIII+HKLNE++KVADQIT+ Sbjct: 151 KALSKKVRLLILDEPTASLNENDSDALLKLLMEFRSQGMTSIIISHKLNEIKKVADQITI 210 Query: 216 LRDGMTVKTLDCHQEEISEDVIIRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHR 275 LRDG TV+TLDCH+E+ISED II MVGR +EDRYPPR+ IG+T+LEVKNWN YHQ HR Sbjct: 211 LRDGGTVETLDCHKEDISEDRIINGMVGRAMEDRYPPREPKIGDTLLEVKNWNVYHQHHR 270 Query: 276 DRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTV 335 DRQ LHD++ VR GEVVGIAGLMGAGRTE AMSVFGKS+GH+ITG+V + G+PVDVST+ Sbjct: 271 DRQFLHDVSFKVRAGEVVGIAGLMGAGRTETAMSVFGKSWGHKITGEVTMHGRPVDVSTI 330 Query: 336 RKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRL 395 KAI AGLAYVTEDRK LGLVL +NI+HNTTLANL V+ +ID+ KE KVA+++R++L Sbjct: 331 PKAIKAGLAYVTEDRKQLGLVLINNIMHNTTLANLHAVASNGVIDERKERKVAAEYRSKL 390 Query: 396 RIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLA 455 RIRS I+QETVNLSGGNQQKVVLSKWLF+NP+VLILDEPTRGID+GAKYEIYTIINQLA Sbjct: 391 RIRSHSIYQETVNLSGGNQQKVVLSKWLFTNPEVLILDEPTRGIDIGAKYEIYTIINQLA 450 Query: 456 ADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSGEKN 511 A+GKG+LMISSEMPELLG CDRIYVMNEGR+VAEL K EASQESIMRAIMRSGEK+ Sbjct: 451 AEGKGILMISSEMPELLGTCDRIYVMNEGRMVAELSKEEASQESIMRAIMRSGEKH 506 Score = 73.2 bits (178), Expect = 2e-17 Identities = 64/248 (25%), Positives = 120/248 (48%), Gaps = 11/248 (4%) Query: 1 MANTILEMRNIT---KTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPA 57 + +T+LE++N + + L +V+ KV+ GE+ + G GAG++ + G Sbjct: 252 IGDTLLEVKNWNVYHQHHRDRQFLHDVSFKVRAGEVVGIAGLMGAGRTETAMSVFGKSWG 311 Query: 58 GTYEGEIHYEGAVRNFRAINDSEDIGIIII---HQELALVPLLSIAENIFLGN--EVASN 112 GE+ G + I + G+ + ++L LV + +I N L N VASN Sbjct: 312 HKITGEVTMHGRPVDVSTIPKAIKAGLAYVTEDRKQLGLVLINNIMHNTTLANLHAVASN 371 Query: 113 GVISWQQTFNRTRELLKKVGLK-ESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPT 171 GVI ++ E K+ ++ S ++ G QQ V ++K L + ++LILDEPT Sbjct: 372 GVIDERKERKVAAEYRSKLRIRSHSIYQETVNLSGGNQQKVVLSKWLFTNPEVLILDEPT 431 Query: 172 ASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEE 231 ++ + ++ + +G ++I+ ++ E+ D+I V+ +G V L +EE Sbjct: 432 RGIDIGAKYEIYTIINQLAAEGKGILMISSEMPELLGTCDRIYVMNEGRMVAELS--KEE 489 Query: 232 ISEDVIIR 239 S++ I+R Sbjct: 490 ASQESIMR 497 Lambda K H 0.316 0.135 0.374 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: 843 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 512 Length of database: 506 Length adjustment: 34 Effective length of query: 478 Effective length of database: 472 Effective search space: 225616 Effective search space used: 225616 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: 52 (24.6 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