Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate AO353_04465 AO353_04465 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04465 Length = 571 Score = 438 bits (1126), Expect = e-127 Identities = 233/494 (47%), Positives = 320/494 (64%), Gaps = 20/494 (4%) Query: 1 MFKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAV 60 M++ + LQ+LGRALM P+A+LP AGLLLR GD DLLNI II DAG V+F NL LIFA+ Sbjct: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI 60 Query: 61 GVAIGLA-GGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIG 119 G+A+G A G AGLA IGYL++ TL K+L I+MG+ GII G Sbjct: 61 GIAVGFARDNNGTAGLAGAIGYLVMVSTL----KVLDAS---------INMGMLAGIISG 107 Query: 120 LLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASSL 179 L+A LY RF I+L L FF G+RFVPI T S++ +GVIF +WP IQ+GIN+ L Sbjct: 108 LMAGALYNRFKDIKLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQL 167 Query: 180 IADS-TVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDP 238 + +S ++G F + RLLI GLHHI +F+ G +TDP+TG VTGDL R+FAGDP Sbjct: 168 LLESGSIGAFVFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDP 227 Query: 239 TAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSF 298 G+FM G FP MIF LPA LA+ A PE++K++ G+ +S ALTS LTG+TEP+EF+F Sbjct: 228 KGGQFMTGMFPMMIFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAF 287 Query: 299 LFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVIPVGIVF 358 +F+AP+LYL++ +L G+ + + ++ G+TFSGG ID L +G STNGW+V PVG+ + Sbjct: 288 MFLAPLLYLLHVLLTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAY 347 Query: 359 AFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDA 418 A IYY +F F I ++NLKTPGRE G EK ++++Q A +QALGG +N+ + A Sbjct: 348 AVIYYVVFDFCIRRFNLKTPGREGVVVG---EKVVLSENQRAGAYIQALGGAENLITVGA 404 Query: 419 CITRLRVTVHQPSQVCKDELKRLGAVGVLE--VNNNFQAIFGTKSDALKDDIKTIMAGGV 476 C TRLR+ + ++ ELK LGA+ V+ + Q + G +D++ D+I+ M Sbjct: 405 CTTRLRLEMVDRNKASDSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAG 464 Query: 477 PATAAALDTVTDKP 490 A AA+ + P Sbjct: 465 SALVAAVVVTEEAP 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: 915 Number of extensions: 50 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: 571 Length adjustment: 37 Effective length of query: 594 Effective length of database: 534 Effective search space: 317196 Effective search space used: 317196 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