Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
Query= SwissProt::P39816 (631 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833 Length = 571 Score = 429 bits (1104), Expect = e-124 Identities = 221/476 (46%), Positives = 318/476 (66%), Gaps = 20/476 (4%) Query: 1 MFKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAV 60 M++ + LQ+LGRALM P+A+LP AGLLLR GD DLLNI II DAG V+F NL +IFA+ Sbjct: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLAMIFAI 60 Query: 61 GVAIGLA-GGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLIDMGVFGGIIIG 119 G+A+G A G AGLA VIGYL++ TL L P I+MG+ GI+ G Sbjct: 61 GIAVGFARDNNGTAGLAGVIGYLVMISTLK------ALDPS-------INMGMLAGIVSG 107 Query: 120 LLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNGINAASSL 179 L+A LY RF I+L L FF G+RFVPI+T +++ +GV+F ++WP IQ+GIN+ +L Sbjct: 108 LMAGALYNRFKDIKLPEYLAFFGGRRFVPIVTGFAAVGLGVVFGYIWPPIQHGINSFGTL 167 Query: 180 IADS-TVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDLTRFFAGDP 238 + +S + G F + RLLI GLHHI +F+ G +TDP+TG VTGDL+R+FAGDP Sbjct: 168 MMESGSFGAFVFGLFNRLLIVTGLHHILNNMAWFVFGNFTDPTTGALVTGDLSRYFAGDP 227 Query: 239 TAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAALTSMLTGITEPVEFSF 298 G+FM G FP MIF LPA LA+ A P ++K++ G+ +S ALT+ LTG+TEP+EF+F Sbjct: 228 KGGQFMTGMFPMMIFGLPAACLAMYRNALPARRKVMGGIFLSMALTAFLTGVTEPIEFAF 287 Query: 299 LFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYGLSTNGWVVIPVGIVF 358 +F+AP+L++++++L G+ + + ++ G+TFSGG ID +L +G STNGW+V PVG+ + Sbjct: 288 MFLAPLLFVLHALLTGLSMAITNALNIHLGFTFSGGFIDMILGWGKSTNGWLVFPVGLAY 347 Query: 359 AFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDA 418 A IYY +F F I +++LKTPGRET D E+ VA ++ A ++ALGG +N+ + A Sbjct: 348 AVIYYVVFDFCIRRFDLKTPGRETSAD---VEQVAVADNERAGAYIKALGGAENLITVGA 404 Query: 419 CITRLRVTVHQPSQVCKDELKRLGAVGVLE--VNNNFQAIFGTKSDALKDDIKTIM 472 C TRLR+ + ++ +LK LGA+ V+ + Q + G +DA+ D+I+ M Sbjct: 405 CTTRLRLDMVDRNKASDTDLKALGAMAVVRPGKGGSLQVVVGPMADAIADEIRLAM 460 Score = 37.0 bits (84), Expect = 2e-06 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 2/71 (2%) Query: 404 LQALGGQQNIANLDA-CITRLRVTVHQPSQVCKDELKRLGAVGVLEVNNN-FQAIFGTKS 461 L ALGG N+ LD +TR+R+ + + + +LK LG GV +++ + + G K+ Sbjct: 492 LNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFDLKALGCQGVSQLDGGIWHLLIGDKA 551 Query: 462 DALKDDIKTIM 472 L D ++ ++ Sbjct: 552 PTLSDALEVLV 562 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: 941 Number of extensions: 49 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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