Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= BRENDA::P09323 (648 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 287 bits (734), Expect = 9e-82 Identities = 168/479 (35%), Positives = 271/479 (56%), Gaps = 41/479 (8%) Query: 6 FFQRLGRALQLPIAVLPVAALLLRFGQ------PDLLNVAFIAQAGGAIFDNLALIFAIG 59 F QRL + L +PIA+LP A +++ PD+ NV ++ G IFD + ++FAI Sbjct: 22 FAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLS-VGKLIFDIMPMLFAIA 80 Query: 60 VASSWSKDSAGAAALAGAVGYFVLTKAMVTI-------------NPEINMGVLAGIITGL 106 VA + +D G AA + A GY VL + P I+ G+ G++ G Sbjct: 81 VAIGFCRDQ-GIAAFSAAFGYGVLLSTLAAAAKVYHLPSHIVWGTPTIDTGIAGGMLVGG 139 Query: 107 VGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWI 166 + A ++LP SFF G+R P+ ++LA + ++WPP+ +I +W Sbjct: 140 ITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDWA 199 Query: 167 V-SAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGT 225 V A+ G +G + RLL+P GLH + N + ++G++ + G + G++ R++AGD + Sbjct: 200 VYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHD-GEIVRGEMARYFAGDPS 258 Query: 226 AGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFM 285 AG G+ I M+GLP AALA++ A + +R V G++LS A ++LTGVTEP+EF F+ Sbjct: 259 AGNLAGGYL-IKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFL 317 Query: 286 FLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGV 345 F+APLLYL HALLTG++ +A LL +H FS G +D+ L++ P +S W + +G Sbjct: 318 FVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLF--PQSSNTHW-IWFLGP 374 Query: 346 IFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDN 405 + F IY+++F I FNLKTPGR EA++ + L + ++A+GG N Sbjct: 375 LTFVIYYILFRASILAFNLKTPGR---------FEADTGQKRNLIAI----VSALGGGGN 421 Query: 406 LKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKK 464 + + AC+TRLR++VAD ++V+ LGA GV+ + +Q++ G KAE++ +++ Sbjct: 422 IADLSACLTRLRISVADPSQVDRQRLMSLGAKGVIVVG-SGVQLVFGTKAETLRKLLQR 479 Lambda K H 0.324 0.139 0.408 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: 661 Number of extensions: 27 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: 648 Length of database: 485 Length adjustment: 36 Effective length of query: 612 Effective length of database: 449 Effective search space: 274788 Effective search space used: 274788 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