GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ngcG in Sinorhizobium meliloti 1021

Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate SMc02871 SMc02871 ABC transporter permease

Query= TCDB::Q8RJU8
         (307 letters)



>FitnessBrowser__Smeli:SMc02871
          Length = 279

 Score =  154 bits (389), Expect = 2e-42
 Identities = 84/267 (31%), Positives = 141/267 (52%), Gaps = 4/267 (1%)

Query: 43  HGILVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSLPDKLHFD--NWSRAWTEAHMGDYF 100
           H  L+ +  + + P+   ++ SFK   +IF  P ++P    F    +     +     YF
Sbjct: 15  HAALIAYTLIALFPVFLTIVNSFKSRNAIFREPLAVPTPETFSLIGYETVLKQGDFIGYF 74

Query: 101 LNTVLVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVN 160
            N+++V   S+   L+ G+MAA+ L+ + F GN  +      G+  PI L  V +   + 
Sbjct: 75  QNSIIVTVVSIALVLLFGAMAAFALSEYRFRGNTLMGLYLALGIMIPIRLGTVAILQGMV 134

Query: 161 NMGLLNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPM 220
             GL+NTL  LILVY A  LP  VF L+ F RT+   +  A  +DG S    F +++LP+
Sbjct: 135 ATGLVNTLTALILVYTAQGLPLAVFILSEFMRTVSDDLKNAGRIDGLSEYAIFLRLVLPL 194

Query: 221 AKPGLISVGIFNFLGQWNQYMLPTVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLV 280
            +P + +V +F  +  WN    P +L      + +T G  Q+ + Q +  +W+ + + L 
Sbjct: 195 IRPAMATVAVFTMIPIWNDLWFPLILAPAEATKTVTLG-SQIFIGQ-FVTNWNAVLSALS 252

Query: 281 MAMLPVLAAYIIFQRQVVQGLTAGALK 307
           +A+ PVL  Y+IF RQ+++G+TAGA+K
Sbjct: 253 LAIFPVLVLYVIFSRQLIRGITAGAVK 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: 257
Number of extensions: 13
Number of successful extensions: 3
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: 279
Length adjustment: 26
Effective length of query: 281
Effective length of database: 253
Effective search space:    71093
Effective search space used:    71093
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