GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcF in Klebsiella michiganensis M5al

Align NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease

Query= TCDB::Q8RJU9
         (308 letters)



>FitnessBrowser__Koxy:BWI76_RS03135
          Length = 290

 Score =  137 bits (344), Expect = 4e-37
 Identities = 91/289 (31%), Positives = 149/289 (51%), Gaps = 24/289 (8%)

Query: 16  PLGLYALLVVW-PFIQSIYYSFTDWTGLSPDFKTVGFDNYERMLDDDIFWKSLQHSLLFA 74
           P  L+ LL  W P  +S+Y S  D   +S   + VG +N+ R+  D +FW+SL ++LL+ 
Sbjct: 13  PSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFADSVFWQSLVNNLLYI 72

Query: 75  LLLPVVTIGLALFFAFMINVGGRRRRGGPVITGVRGSGFYKIVYFFPQVLSIAIVALLFA 134
           LL  V  + LAL  A  +    R  R            + +  +FFP ++ +   A L+ 
Sbjct: 73  LLTVVPGVTLALLLAVALTENHRVNR------------WLRTAFFFPMIIPMVSAAALWL 120

Query: 135 FAYNPDSGAINSLLRGIGLGDVQPVWLGDPDLALWCVMAVIVWSTVGFFVVLFSAGMASI 194
           F + P  G ++  L  +  G +   WLG  + AL  +  + VW   G++++ F AG+ SI
Sbjct: 121 FIFMPGLGLLDHYLAKL-FGPMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQSI 179

Query: 195 PADIYEAALLDGANRVTTFFRITLPLLWDTVQSGWVYMGILALGAESFAVVHIMTTGPGG 254
           PA   EAA+++GA R   FF++TLPLL  T+     ++   AL      + H+     GG
Sbjct: 180 PASTREAAIMEGATRTQVFFKVTLPLLRPTLS----FVITTALIYSITQIDHVAVMTRGG 235

Query: 255 PDYSTTVMVLYVYQKAFRD---GQAAYATTIGVALLIVTLAFAAVVMRL 300
           PD +TTV++ Y+   A+     G+A+ AT + +A L    AF+ + ++L
Sbjct: 236 PDNATTVLLYYIQNLAWDTHDLGKASAATFLTLAGL---FAFSLINLKL 281


Lambda     K      H
   0.330    0.145    0.458 

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: 277
Number of extensions: 16
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: 308
Length of database: 290
Length adjustment: 27
Effective length of query: 281
Effective length of database: 263
Effective search space:    73903
Effective search space used:    73903
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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