Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__MR1:200788 Length = 499 Score = 307 bits (787), Expect = 6e-88 Identities = 173/468 (36%), Positives = 268/468 (57%), Gaps = 18/468 (3%) Query: 6 FQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDA-----GGVVFDNLPLIFAV 60 F+ Q+L +AL+ P+A+LPAAG++L + +P + + G ++F +P++FAV Sbjct: 25 FKFAQRLSQALLIPIAILPAAGVMLGLTVSPIPFMPEVLNVLMLAVGKLIFAIMPILFAV 84 Query: 61 GVAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGL 120 VAIG +G+A AV GY ++T TL + L L +D G+ GG++IG Sbjct: 85 AVAIGFCRDQGIAAFTAVFGYGVMTATLAALADLYQLPTQLVLGMETLDTGIAGGMLIGG 144 Query: 121 LAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASSLI 180 + + + I L + FF G+R ++ ++ +G + + +WP + I S Sbjct: 145 VTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLSLLIERVSDWA 204 Query: 181 ADSTVGLFF--YATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDP 238 + F Y + RLLIP GLHHI+ PFY +G+Y V G++ R+ AGDP Sbjct: 205 VYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQY-QLQDAEVVRGEVARYLAGDP 263 Query: 239 TAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSF 298 AG + G + ++ LPA ALAI A ++ ++G+M+SAA S LTG+TEP+EF+F Sbjct: 264 QAGN-LAGGYLIKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFAF 322 Query: 299 LFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTN-GWVVIPVGIV 357 +FVAP+L+LI+ +L+G+ + VC + + H FS G +D+ L + LS N GW + +G + Sbjct: 323 MFVAPLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFAV-LGPL 381 Query: 358 FAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLD 417 A IYY LFR +IL +NLKTPGR DG K + ++ ALGG+ NI L+ Sbjct: 382 TAVIYYILFRGSILAFNLKTPGR-LQSDGTKGSKESLRA------IIAALGGRDNIVELN 434 Query: 418 ACITRLRVTVHQPSQVCKDELKRLGAVGVLEVNNNFQAIFGTKSDALK 465 AC+TRLR++VH P V K L +LGA GV+ + Q ++GTK++ L+ Sbjct: 435 ACLTRLRLSVHSPELVNKVRLSQLGAKGVIVMGKGVQIVYGTKAETLR 482 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: 712 Number of extensions: 36 Number of successful extensions: 4 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: 499 Length adjustment: 36 Effective length of query: 595 Effective length of database: 463 Effective search space: 275485 Effective search space used: 275485 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