GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TRIC in Shewanella amazonensis SB2B

Align putative transporter, required for glycine and L-alanine utilization (characterized)
to candidate 6936665 Sama_0852 hypothetical protein (RefSeq)

Query= reanno::ANA3:7023996
         (213 letters)



>FitnessBrowser__SB2B:6936665
          Length = 207

 Score =  162 bits (411), Expect = 3e-45
 Identities = 86/204 (42%), Positives = 130/204 (63%), Gaps = 11/204 (5%)

Query: 12  LIGILAEAMTGALAAGRKQMDLFGVVIIGCATAIGGGTLRDMLLGNYPLIWVENVHYLLA 71
           L G    A+TGALAAGR +MD FGV ++   TA+GGGT+RD ++G  P+ W+ + +YL+ 
Sbjct: 9   LCGTAVFALTGALAAGRHRMDPFGVTVLAAVTAVGGGTIRDAIIGATPVFWLRDPNYLIV 68

Query: 72  IAFASLLTVAIAPVMRYLSKLFLAI-DALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTG 130
           I      T+      R + +  L I DALGLA+F+++GAQK L LG +   AV+MGL+TG
Sbjct: 69  ILATVGFTLVFIRRPRKVPQYTLPIADALGLALFTVIGAQKALSLGLNGMSAVIMGLITG 128

Query: 131 VFGGVIRDILCNQVPLIFKKELYAVISL-----FTAGLYITLNAYQLAEWINLVVCLTLG 185
           V GG+IRD+LC Q+P++ + E+YA  S+     +T  L + +N+ Q A W++++  L   
Sbjct: 129 VGGGIIRDVLCRQIPMVLRTEIYATASILGGIAYTLSLQLGMNS-QTALWLSMLSALI-- 185

Query: 186 FSLRMLALRYHWSMPTFDYQANGD 209
             LR+ A+R+H S+P FD +   D
Sbjct: 186 --LRLAAIRWHLSLPAFDLKTRRD 207



 Score = 38.1 bits (87), Expect = 1e-07
 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 93  FLAIDALGLAVFSIVGAQKTLMLGFSPTIAVVMGLVTGVFGGVIRDILCNQVPLIFKKE- 151
           F   D  G AVF++ GA         P    V+  VT V GG IRD +    P+ + ++ 
Sbjct: 4   FYFFDLCGTAVFALTGALAAGRHRMDPFGVTVLAAVTAVGGGTIRDAIIGATPVFWLRDP 63

Query: 152 LYAVISLFTAG 162
            Y ++ L T G
Sbjct: 64  NYLIVILATVG 74


Lambda     K      H
   0.330    0.143    0.438 

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: 152
Number of extensions: 7
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 213
Length of database: 207
Length adjustment: 21
Effective length of query: 192
Effective length of database: 186
Effective search space:    35712
Effective search space used:    35712
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: 45 (21.9 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