Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (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::O34521 (452 letters) >FitnessBrowser__Burk376:H281DRAFT_01853 Length = 596 Score = 359 bits (922), Expect = e-103 Identities = 203/477 (42%), Positives = 284/477 (59%), Gaps = 32/477 (6%) Query: 5 LQKLGKSFMLPIAVLPAVGIILALGREDVFN------IPFVYQAGTAVFDHLPLIFAIGI 58 LQK+GKS MLP+AVLP G++L LG D + + AG +F +LPLIFAIG+ Sbjct: 9 LQKVGKSLMLPVAVLPVAGLLLGLGATDFHGYVPAIVLALMKNAGDVIFANLPLIFAIGV 68 Query: 59 AIGISKDSNGAAGLSGAISYLMLDAATKTIDKTNNM-------------AVFGGIIAGLI 105 A+G + +++G +G++ I YL++ A I K + VFGGI+AG + Sbjct: 69 ALGFT-ENDGVSGIAATIGYLVMTATLGVIAKVEGIEPDMIMGIPSIQTGVFGGILAGGL 127 Query: 106 AGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWM- 164 A + +NR+ LP YLGFF+G+R VPI+TAI +I+L I VVWPPI S I +F +W Sbjct: 128 AAWMFNRYYRIALPAYLGFFAGKRFVPIVTAIGSIVLGAILSVVWPPIGSAIKAFSQWAA 187 Query: 165 LGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYNGVT------GDLARFFAKDPT 218 + A ++G RLLIP GLHH+ N F+F+ G + T GD+ RFFA D T Sbjct: 188 VSDPRTAATVYGFVERLLIPFGLHHIWNVPFFFEAGSFLDPTTGKVVHGDITRFFAGDRT 247 Query: 219 AGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFM 278 AG + G F MFGLPAA +A+ AKP + A GMM+ ALT+F+TGITEPIEFAF+ Sbjct: 248 AGI-LAGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITEPIEFAFL 306 Query: 279 FLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPL---LLLLVGI 335 F++P+LY +HA L + F+ N LG+R GF+FS G ID+++ I K + ++G Sbjct: 307 FVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAWYVFILGP 366 Query: 336 CYAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTID 395 YA +Y+ VF +I +LKTPGREDD V+ ++ GG+ N+ ++D Sbjct: 367 IYAVIYYGVFRFVITRFDLKTPGREDDTVETAKVSTAGVGGRSRELVLAFGGRSNIDSLD 426 Query: 396 HCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEELRAAVK 452 C TRLR++VK+ ALV+E LK GA GVV+ G VQ I GP E ++ +K Sbjct: 427 ACITRLRISVKNPALVNEGKLKALGAAGVVRV-GNGVQAIFGPLSENMKTDMHEYLK 482 Score = 35.4 bits (80), Expect = 5e-06 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 1/65 (1%) Query: 385 LGGKENLQTIDH-CATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFA 443 LGG N+Q +D ATRLR+ ++D + +D A LK AG +I+G + Sbjct: 532 LGGVANIQKLDALAATRLRVGLRDASQLDTAALKAAGVPATQTLTNGEFDLIVGLDAPNL 591 Query: 444 AEELR 448 A +R Sbjct: 592 AGAMR 596 Lambda K H 0.326 0.144 0.429 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: 696 Number of extensions: 45 Number of successful extensions: 10 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: 452 Length of database: 596 Length adjustment: 35 Effective length of query: 417 Effective length of database: 561 Effective search space: 233937 Effective search space used: 233937 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 (21.6 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