Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__PV4:5210198 Length = 490 Score = 302 bits (774), Expect = 2e-86 Identities = 167/467 (35%), Positives = 264/467 (56%), Gaps = 19/467 (4%) Query: 6 FQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIP-----IIKDAGGVVFDNLPLIFAV 60 F+ Q+L +AL+ P+A+LPAAG+++ + I ++ G +VF +P++FAV Sbjct: 24 FKFAQRLSQALLLPIAILPAAGVMIGLATNPIPFISADLATLMWTVGNLVFSMMPMLFAV 83 Query: 61 GVAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIGL 120 +AIG +G+A +AV GY + +L + K+ L + ID G+ GG+++G Sbjct: 84 TIAIGFCRDQGIAAFSAVFGYGVFFSSLSALAKIYHLPTEMILGQATIDTGIAGGMMVGA 143 Query: 121 LAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASS-- 178 + K I L V FF G+R P++ ++++ +F +WPL+ N I S+ Sbjct: 144 FTCLVVKHSERIRLPAVFSFFEGRRSAPLLMLPMAILLAYLFLLLWPLLSNWIEQISNWA 203 Query: 179 LIADSTVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDP 238 + + Y + RLLIP GLHHI+ PFY MG+Y + V G++ R+ AGDP Sbjct: 204 VYQEPASAFAVYGMVERLLIPLGLHHIWNAPFYLEMGQYFNGD--EWVRGEVARYLAGDP 261 Query: 239 TAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSF 298 AG + G + ++ LPA ALAI A ++ ++G+M+SAA LTG+TEP+EF+F Sbjct: 262 QAGN-LAGGYLIKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFAF 320 Query: 299 LFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVIPVGIVF 358 +FVAP+L+++++++ G+ + V + H FS G +D+ L G S N + +G + Sbjct: 321 MFVAPLLFILHALMTGIAYAVTISLDIHHSVVFSHGLVDFSLLLGQSRNVEWFLILGPLT 380 Query: 359 AFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDA 418 A IYY +FR AIL +NLKTPGR GQ ++ ALGGQ NI L A Sbjct: 381 AVIYYLVFRGAILAFNLKTPGRMEAGSGQRAG---------LISMITALGGQDNINELTA 431 Query: 419 CITRLRVTVHQPSQVCKDELKRLGAVGVLEVNNNFQAIFGTKSDALK 465 C+TRLR++V V K +L +LGA GV+ V N Q ++GTK+++++ Sbjct: 432 CLTRLRISVKHAELVDKAQLNKLGAKGVVLVGNGVQLVYGTKAESIR 478 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: 701 Number of extensions: 37 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: 490 Length adjustment: 36 Effective length of query: 595 Effective length of database: 454 Effective search space: 270130 Effective search space used: 270130 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