GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutW in Sinorhizobium meliloti 1021

Align ABC transporter for L-Histidine, permease component (characterized)
to candidate SMc02379 SMc02379 permease

Query= reanno::pseudo5_N2C3_1:AO356_09615
         (283 letters)



>lcl|FitnessBrowser__Smeli:SMc02379 SMc02379 permease
          Length = 295

 Score =  273 bits (697), Expect = 4e-78
 Identities = 133/257 (51%), Positives = 187/257 (72%)

Query: 20  SLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVGGIAWHATRKVLATAVIVGL 79
           S    YGD      D L + +++ E  +   PW ++L ++  IAW A+R     A  +G 
Sbjct: 28  SFTRAYGDAIESFFDPLQFFLIHAERFMTRTPWPIILILIAVIAWFASRNWKIVAGAIGT 87

Query: 80  LFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSARSNRLRSVLMPLLDIMQTMPS 139
           L L+G + +WD  M+T++++ V T++S+ IGIP+GI+ +RS+R ++++ P+LD+MQTMPS
Sbjct: 88  LLLIGYLDMWDDTMKTISMIFVCTVLSIAIGIPMGIIMSRSDRFQNIVNPVLDVMQTMPS 147

Query: 140 FVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQVDGEVMEAINAFGANRWQQL 199
           FVYLIPV+ML G+GKVP + A VIYA PP+IRLT+LGIR VD +V+EA +AFG++ WQ+L
Sbjct: 148 FVYLIPVVMLLGIGKVPGLIAVVIYAIPPMIRLTNLGIRLVDKDVLEAADAFGSSNWQKL 207

Query: 200 FGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGEDVLVGIQTLNVGRGLEAGLA 259
             VQ+PLALP+IMAGINQT MMAL+MVVIASMIG +GLG+ VL  I       G+  GLA
Sbjct: 208 KNVQMPLALPTIMAGINQTIMMALAMVVIASMIGVQGLGQPVLKAIANQYFTLGIFNGLA 267

Query: 260 IVILAVVIDRITQAYGR 276
           IV +A++ DR++QAYGR
Sbjct: 268 IVGIAIIFDRVSQAYGR 284


Lambda     K      H
   0.328    0.142    0.429 

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: 294
Number of extensions: 10
Number of successful extensions: 1
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: 283
Length of database: 295
Length adjustment: 26
Effective length of query: 257
Effective length of database: 269
Effective search space:    69133
Effective search space used:    69133
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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