Align PTS system N-acetylglucosamine-specific EIIB component; PTS system GlcNAc-specific EIIB component; N-acetylglucosamine-specific phosphotransferase enzyme IIB component; GlcNAc-specific phosphotransferase enzyme IIB 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::Q9S2H6 (77 letters) >FitnessBrowser__Burk376:H281DRAFT_01853 Length = 596 Score = 68.6 bits (166), Expect = 7e-17 Identities = 30/77 (38%), Positives = 49/77 (63%) Query: 1 MASKAEKIVAGLGGIDNIDEIEGCITRLRTEVNDPALVNEAALKAAGAHGVVKMGTAIQV 60 + ++ ++V GG NID ++ CITRLR V +PALVNE LKA GA GVV++G +Q Sbjct: 405 VGGRSRELVLAFGGRSNIDSLDACITRLRISVKNPALVNEGKLKALGAAGVVRVGNGVQA 464 Query: 61 VIGTDADPIAAEIEDMM 77 + G ++ + ++ + + Sbjct: 465 IFGPLSENMKTDMHEYL 481 Score = 43.9 bits (102), Expect = 2e-09 Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 2/71 (2%) Query: 2 ASKAEKIVAGLGGIDNIDEIEG-CITRLRTEVNDPALVNEAALKAAGAHGVVKMGTA-IQ 59 A + EKI A LGG+ NI +++ TRLR + D + ++ AALKAAG + Sbjct: 522 AERVEKIRAALGGVANIQKLDALAATRLRVGLRDASQLDTAALKAAGVPATQTLTNGEFD 581 Query: 60 VVIGTDADPIA 70 +++G DA +A Sbjct: 582 LIVGLDAPNLA 592 Lambda K H 0.315 0.133 0.360 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: 115 Number of extensions: 4 Number of successful extensions: 3 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: 77 Length of database: 596 Length adjustment: 21 Effective length of query: 56 Effective length of database: 575 Effective search space: 32200 Effective search space used: 32200 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: 42 (22.0 bits) S2: 45 (21.9 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