GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Azospirillum brasilense Sp245

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate AZOBR_RS27985 AZOBR_RS27985 ABC transporter permease

Query= TCDB::Q8RJU8
         (307 letters)



>FitnessBrowser__azobra:AZOBR_RS27985
          Length = 280

 Score =  132 bits (333), Expect = 7e-36
 Identities = 82/271 (30%), Positives = 135/271 (49%), Gaps = 18/271 (6%)

Query: 43  HGILVLWAFMVVLPLLWAVMTSFK------DDASIFGSPWSLPDKLHFDNWSRAWTEAHM 96
           H   +    +V+ P  W V  + +      DDA +F     LP     +N+   W + H 
Sbjct: 21  HAAALALLLLVLFPFAWMVQMALRPADAVLDDAVLF-----LPT---LENFVALW-QGHF 71

Query: 97  GDYFLNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLF 156
              FLN+VLV   S   +L LG  AAYVL R+ F   R +    +     P +   +P F
Sbjct: 72  PKSFLNSVLVSSLSTAASLALGVPAAYVLTRWRFRARRRVALWILATRMAPPIALTIPFF 131

Query: 157 YVVNNMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQI 216
                +GL +++ GL L+Y+ +++   V+F+  FF  +P S+ EAA++DG    + F ++
Sbjct: 132 LAYRWVGLQDSVVGLALIYMTFNISIVVWFMQTFFAAIPRSLEEAAWIDGCGVWQAFRRV 191

Query: 217 MLPMAKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLF 276
            LP+A PGL +  +F F+  WN +    +L T  +       +      +G+  +W  + 
Sbjct: 192 TLPLAAPGLAATAVFCFIFSWNDFFFALIL-TRTNAVTAPVAITNFLQYEGW--EWGKIA 248

Query: 277 AGLVMAMLPVLAAYIIFQRQVVQGLTAGALK 307
           A   + MLPVLA  ++ ++ +V+GLTAG LK
Sbjct: 249 AAGTLVMLPVLAFTLLVRKYLVRGLTAGGLK 279


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: 241
Number of extensions: 16
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: 280
Length adjustment: 26
Effective length of query: 281
Effective length of database: 254
Effective search space:    71374
Effective search space used:    71374
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