Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 319 bits (818), Expect = 2e-91 Identities = 176/467 (37%), Positives = 270/467 (57%), Gaps = 19/467 (4%) Query: 6 FQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIP-----IIKDAGGVVFDNLPLIFAV 60 F+ Q+L + L+ P+A+LPAAG+++ L IP ++ G ++FD +P++FA+ Sbjct: 20 FRFAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLSVGKLIFDIMPMLFAI 79 Query: 61 GVAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGL 120 VAIG +G+A +A GY +L TL K+ L ID G+ GG+++G Sbjct: 80 AVAIGFCRDQGIAAFSAAFGYGVLLSTLAAAAKVYHLPSHIVWGTPTIDTGIAGGMLVGG 139 Query: 121 LAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAAS--S 178 + + + L V FF G+R P+I +++ V+ +F+WP + I S + Sbjct: 140 ITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDWA 199 Query: 179 LIADSTVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDP 238 + + + FY + RLL+P GLHHI+ PFY +G+Y G V G++ R+FAGDP Sbjct: 200 VYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHD--GEIVRGEMARYFAGDP 257 Query: 239 TAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSF 298 +AG + G + ++ LPA ALAI A ++ ++GVM+SAA S LTG+TEP+EF+F Sbjct: 258 SAGN-LAGGYLIKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAF 316 Query: 299 LFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVIPVGIVF 358 LFVAP+LYL +++L G+ + + L + H FS G +D+VL + S+N + +G + Sbjct: 317 LFVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHWIWFLGPLT 376 Query: 359 AFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDA 418 IYY LFR +IL +NLKTPGR + GQ ++ ALGG NIA+L A Sbjct: 377 FVIYYILFRASILAFNLKTPGRFEADTGQKRN---------LIAIVSALGGGGNIADLSA 427 Query: 419 CITRLRVTVHQPSQVCKDELKRLGAVGVLEVNNNFQAIFGTKSDALK 465 C+TRLR++V PSQV + L LGA GV+ V + Q +FGTK++ L+ Sbjct: 428 CLTRLRISVADPSQVDRQRLMSLGAKGVIVVGSGVQLVFGTKAETLR 474 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: 726 Number of extensions: 31 Number of successful extensions: 5 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: 485 Length adjustment: 36 Effective length of query: 595 Effective length of database: 449 Effective search space: 267155 Effective search space used: 267155 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