GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Synechococcus elongatus PCC 7942

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like

Query= TCDB::Q8RJU8
         (307 letters)



>FitnessBrowser__SynE:Synpcc7942_0471
          Length = 276

 Score =  172 bits (435), Expect = 1e-47
 Identities = 91/260 (35%), Positives = 150/260 (57%), Gaps = 6/260 (2%)

Query: 50  AFMVVLPLLWAVMTSFKDDAS-IFG-SPWSLPDKLHFDNWSRAWTEAHMGDYFLNTVLVV 107
           A  +++PLLW V T+FK     IF   P  LP +   DN+ R WTE  +G YFLN+  V 
Sbjct: 20  AVAMLIPLLWLVSTAFKSAGEDIFQFPPQFLPTQPTLDNFRRVWTENPLGQYFLNSTWVA 79

Query: 108 GGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNMGLLNT 167
             ++   L+  S+AAY LAR +F G + ++ L +  +  P  + ++PL+ ++ N+GL NT
Sbjct: 80  LLTVGLNLLFCSLAAYPLARLEFKGRQTLFLLIVATILIPFQVVMIPLYVLIINLGLRNT 139

Query: 168 LHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAKPGLIS 227
             GL+  Y+A +  F +F L   F+ +P  + EAA +DG +    ++ +M+P A+P LI+
Sbjct: 140 YLGLVFPYLASA--FGIFLLRQAFQGIPKDLEEAARIDGCNDLGVWWNVMIPSARPALIT 197

Query: 228 VGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMAMLPVL 287
           + IF F+G W+ ++ P ++  +PD+  L  G+  LA   G+  DW  + AG V+++LPV 
Sbjct: 198 LAIFVFIGSWSDFLWPLIILDEPDRYTLPLGIATLA--SGFSLDWRLVAAGSVLSILPVF 255

Query: 288 AAYIIFQRQVVQGLTAGALK 307
             ++  QR +V    A  +K
Sbjct: 256 GVFLALQRYIVPSAAASGVK 275


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: 274
Number of extensions: 17
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: 307
Length of database: 276
Length adjustment: 26
Effective length of query: 281
Effective length of database: 250
Effective search space:    70250
Effective search space used:    70250
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