GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07310 in Sinorhizobium meliloti 1021

Align Inositol transport system permease protein (characterized)
to candidate SMa0070 SMa0070 ABC transporter permease

Query= reanno::Phaeo:GFF716
         (373 letters)



>FitnessBrowser__Smeli:SMa0070
          Length = 327

 Score =  170 bits (431), Expect = 4e-47
 Identities = 116/351 (33%), Positives = 172/351 (49%), Gaps = 52/351 (14%)

Query: 26  RPELGGIIGTITVFAMFLIFAGDSGMF-----NSQGVMNWSQISAQFMIIAVGACLLMIA 80
           +PEL G+     +F + L+F   S        N +GVM    +  +  ++A+G  LLMI 
Sbjct: 11  KPELAGLA---LLFVLVLVFQAKSNGILLSFENMRGVMG---LLPEMALVAIGVTLLMIC 64

Query: 81  GEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFIVVRTGLPSFI 140
           GEFDLSVGS+     M +A+  +  G P  +A+L+   I  AIG +NG++ ++  +PSFI
Sbjct: 65  GEFDLSVGSVFALMPMSMAVL-LNSGVPFTVAVLLGLMICGAIGFINGYVTLQFSIPSFI 123

Query: 141 VTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGD---WLAALFGGKILTGLFQWFGDN 197
            TL  LFI R   I          I GG       D   WL               F D 
Sbjct: 124 TTLGMLFIARSLTI---------VISGGFPPLLPPDLPTWL---------------FTDY 159

Query: 198 GWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGDAEAARNS 257
            W         +G P      M  +W +++  +   +L+ T FGNWI A GG  EAA + 
Sbjct: 160 IW---------QGSP----FRMSFLWFVVIAALVAALLSLTNFGNWIRATGGFNEAAASM 206

Query: 258 GVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGGALLTGGY 317
           G+PV RVKI+ FM  +  A      QV+  G      G   E +A+ A VIGG  L GG 
Sbjct: 207 GIPVKRVKIVCFMLCSVLAGFAGLLQVLRLGSPLPSIGEGLELQAVAAAVIGGTALAGGI 266

Query: 318 GSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNTYIRRV 368
           G+V GA +G L+   +  GL  + V+++ F+  +G++ +FAVI N ++ ++
Sbjct: 267 GTVFGAIIGTLLIRTIDNGLVLSRVDANWFKFAIGVLTMFAVIANAWMGKM 317


Lambda     K      H
   0.330    0.145    0.443 

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: 449
Number of extensions: 28
Number of successful extensions: 3
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: 373
Length of database: 327
Length adjustment: 29
Effective length of query: 344
Effective length of database: 298
Effective search space:   102512
Effective search space used:   102512
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: 49 (23.5 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