Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__Burk376:H281DRAFT_01853 Length = 596 Score = 437 bits (1124), Expect = e-127 Identities = 243/508 (47%), Positives = 331/508 (65%), Gaps = 23/508 (4%) Query: 1 MFKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDL------LNIPIIKDAGGVVFDNL 54 +FK AF +LQ++G++LM PVAVLP AGLLL G D + + ++K+AG V+F NL Sbjct: 1 VFKHAFGVLQKVGKSLMLPVAVLPVAGLLLGLGATDFHGYVPAIVLALMKNAGDVIFANL 60 Query: 55 PLIFAVGVAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFG 114 PLIFA+GVA+G +GV+G+AA IGYL++T TL + K+ G++P I GVFG Sbjct: 61 PLIFAIGVALGFTENDGVSGIAATIGYLVMTATLGVIAKVEGIEPDMIMGIPSIQTGVFG 120 Query: 115 GIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGIN 174 GI+ G LAA+++ R+ I L LGFF+GKRFVPI+T++ S+V+G I S VWP I + I Sbjct: 121 GILAGGLAAWMFNRYYRIALPAYLGFFAGKRFVPIVTAIGSIVLGAILSVVWPPIGSAIK 180 Query: 175 AAS--SLIADSTVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTR 232 A S + ++D Y + RLLIPFGLHHI+ PF+F G + DP+TG V GD+TR Sbjct: 181 AFSQWAAVSDPRTAATVYGFVERLLIPFGLHHIWNVPFFFEAGSFLDPTTGKVVHGDITR 240 Query: 233 FFAGDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITE 292 FFAGD TAG + G F + +F LPA A+AI H A+PE K + G+M+SAALTS LTGITE Sbjct: 241 FFAGDRTAG-ILAGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITE 299 Query: 293 PVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYV---LNYGLSTNGW 349 P+EF+FLFVAPVLYLI++ LA V + +R G+TFS GGID++ L ST+ W Sbjct: 300 PIEFAFLFVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAW 359 Query: 350 VVIPVGIVFAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGG 409 V +G ++A IYY +FRF I +++LKTPGRE D+ + + + + ++ A GG Sbjct: 360 YVFILGPIYAVIYYGVFRFVITRFDLKTPGRE-DDTVETAKVSTAGVGGRSRELVLAFGG 418 Query: 410 QQNIANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEVNNNFQAIFGTKSDALKDD-- 467 + NI +LDACITRLR++V P+ V + +LK LGA GV+ V N QAIFG S+ +K D Sbjct: 419 RSNIDSLDACITRLRISVKNPALVNEGKLKALGAAGVVRVGNGVQAIFGPLSENMKTDMH 478 Query: 468 --IKT------IMAGGVPATAAALDTVT 487 +KT + A G AA T T Sbjct: 479 EYLKTAGSEADLAADGKAVAEAAASTAT 506 Lambda K H 0.324 0.142 0.421 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: 956 Number of extensions: 59 Number of successful extensions: 7 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: 631 Length of database: 596 Length adjustment: 37 Effective length of query: 594 Effective length of database: 559 Effective search space: 332046 Effective search space used: 332046 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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