Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate BWI76_RS27535 BWI76_RS27535 PTS transporter subunit IIBC
Query= SwissProt::O34521 (452 letters) >FitnessBrowser__Koxy:BWI76_RS27535 Length = 519 Score = 210 bits (534), Expect = 1e-58 Identities = 159/507 (31%), Positives = 239/507 (47%), Gaps = 76/507 (14%) Query: 1 MLSFLQKLGKSFMLPIAVLPAVGIILALGR-----EDVFNIPFVYQAGTAV-------FD 48 +L +QK ++ + + LP +G+ILAL + F++Q G + F Sbjct: 8 ILENMQKFSRAMIGAVLFLPVIGLILALSSVLTNPTLISETSFLHQLGQLLGDTFWPLFG 67 Query: 49 HLPLIFAIGIAIGISKDSNGAAGLSGAISYLMLDAATKT--------IDKTN-------- 92 +L L+F +GI+ G++KD L + ++M A + +K N Sbjct: 68 NLGLLFCVGISYGLAKDKKTEVALVSVMCFIMFLGANHSWLEHTHGLAEKINGEYYGTGQ 127 Query: 93 ---------NMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILA 143 +M VF GII G + +N+ +LP L + G +L + + I A Sbjct: 128 TQLLGFVVVDMGVFLGIILGCTIAWVHNKVSTIELPGALSMYGGAKLTLVAMTPVVIFYA 187 Query: 144 GIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFW--FQFGE 201 F WP + I + +M G G ++G F + LIP GLHH + W FQ + Sbjct: 188 IAFTWFWPFMTHGIAALTGFMKNAGVAGVFVYGFFEKFLIPTGLHHFV----WSPFQLTQ 243 Query: 202 YNG--------VTGDLARFFA--KDPTAGTYMTGFFPIM------MFGLPAACLAMVVTA 245 G V+G A F A + P M +FGL A LA TA Sbjct: 244 IGGTLSVDGQVVSGTQAIFLAYMRHPDLTPVMNEALRFSQQGMTTIFGLAGASLAFYHTA 303 Query: 246 KPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLGIR 305 KP K+ +++ +T+ +TGITEPIEF F+F+SPLL+ +HA LT S I + +R Sbjct: 304 KPEKKMMAKAILLPAIITSMLTGITEPIEFTFLFVSPLLWVIHATLTAASQAICDIFTVR 363 Query: 306 SGFSFSAGAIDYVLSYGIAEKPLL-----LLLVGICYAAVYFIVFYVLIKALNLKTPGRE 360 + A + L Y + L +L+GI AVY+++F L+ LNLKTPGRE Sbjct: 364 ---PWGASGLIEFLIYNLPLPVSLTRWPGYVLIGIGQFAVYYVIFRTLVVKLNLKTPGRE 420 Query: 361 DDD-------VDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDE 413 DD+ D Q V N ++ GLGGKEN+ ++D+C TRLR+ + + LVD+ Sbjct: 421 DDENVKLYSKADYRKKMGEPQSVT-NEIINGLGGKENIISVDNCFTRLRVAIHNMDLVDD 479 Query: 414 ALLKKAGAKGVVKSGGQSVQVIIGPNV 440 +LK GA GVV++ + VQVI G V Sbjct: 480 TILKSTGANGVVRNRNE-VQVIYGVKV 505 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: 561 Number of extensions: 29 Number of successful extensions: 6 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: 452 Length of database: 519 Length adjustment: 34 Effective length of query: 418 Effective length of database: 485 Effective search space: 202730 Effective search space used: 202730 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