GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Herbaspirillum seropedicae SmR1

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate HSERO_RS01335 HSERO_RS01335 sugar ABC transporter permease

Query= TCDB::Q8RJU8
         (307 letters)



>FitnessBrowser__HerbieS:HSERO_RS01335
          Length = 283

 Score =  145 bits (367), Expect = 8e-40
 Identities = 91/286 (31%), Positives = 152/286 (53%), Gaps = 9/286 (3%)

Query: 25  PAPPQKEKKEGTVLNVFSHGI-LVLWAFMVVLPLLWAVMTSFK-DDASIFGSPWSLP-DK 81
           P P +K K     L   S  + L++W    +LP+L A++TS + +D  + G+ W  P D 
Sbjct: 3   PMPIEKWKPINRALYRASLPVALLIW----LLPMLAALVTSIRSNDELMAGNYWGWPQDF 58

Query: 82  LHFDNWSRAWTEAHMGDYFLNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFI 141
              +N+  A T + M  YF N+ L+   S+IG + L +MA + L+ + F GN  ++  F+
Sbjct: 59  AMLENYREALTASPMLHYFWNSCLITIPSVIGAISLAAMAGFALSTYQFRGNTVLFATFV 118

Query: 142 GGMSFPIMLALVPLFYVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEA 201
                P  + ++P+  +  ++GL NT+ G++L +IA    F   FL  F + LP  + EA
Sbjct: 119 ACNFVPQQILMIPVRDLSLSLGLFNTITGMMLFHIAMQTGFCTLFLRNFIKQLPFEMIEA 178

Query: 202 AFVDGASHTRTFFQIMLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQ 261
           A ++GAS    F++I+LP+ +P L ++ +  F   WN Y    VL    D   +T G+  
Sbjct: 179 ARIEGASEWTVFYRIVLPLIRPALAALAVLVFTFVWNDYFWALVLTQGDDVAPITVGVA- 237

Query: 262 LAVSQGYKGDWSGLFAGLVMAMLPVLAAYIIFQRQVVQGLTAGALK 307
            A+   +   W+ + AG ++A LP +  + + Q+Q V GLT GA K
Sbjct: 238 -ALRGQWTTAWNLVSAGSILAALPSVILFFVMQKQFVAGLTFGASK 282


Lambda     K      H
   0.326    0.141    0.440 

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: 263
Number of extensions: 12
Number of successful extensions: 2
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: 307
Length of database: 283
Length adjustment: 26
Effective length of query: 281
Effective length of database: 257
Effective search space:    72217
Effective search space used:    72217
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 (21.6 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