GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrT in Shewanella sp. ANA-3

Align sucrose permease scrT (characterized)
to candidate 7022816 Shewana3_0067 major facilitator transporter (RefSeq)

Query= reanno::ANA3:7022816
         (406 letters)



>FitnessBrowser__ANA3:7022816
          Length = 406

 Score =  802 bits (2071), Expect = 0.0
 Identities = 406/406 (100%), Positives = 406/406 (100%)

Query: 1   MVSDSNSVENRHHTRIRVLTYLMFFMFAMTSDAVGVIIPQLISEFGLSLSQASAFHYMPM 60
           MVSDSNSVENRHHTRIRVLTYLMFFMFAMTSDAVGVIIPQLISEFGLSLSQASAFHYMPM
Sbjct: 1   MVSDSNSVENRHHTRIRVLTYLMFFMFAMTSDAVGVIIPQLISEFGLSLSQASAFHYMPM 60

Query: 61  IFIAISGLFLGFLADKIGRKLTILLGLLLFAIACFLFALGESFYYFLLLLALVGLAIGVF 120
           IFIAISGLFLGFLADKIGRKLTILLGLLLFAIACFLFALGESFYYFLLLLALVGLAIGVF
Sbjct: 61  IFIAISGLFLGFLADKIGRKLTILLGLLLFAIACFLFALGESFYYFLLLLALVGLAIGVF 120

Query: 121 KTGALALIGDISRSTKQHSSTMNTVEGFFGVGAMVGPAIVSYLLISGVSWKYLYFGAGVF 180
           KTGALALIGDISRSTKQHSSTMNTVEGFFGVGAMVGPAIVSYLLISGVSWKYLYFGAGVF
Sbjct: 121 KTGALALIGDISRSTKQHSSTMNTVEGFFGVGAMVGPAIVSYLLISGVSWKYLYFGAGVF 180

Query: 181 CLLLCWLAFRADYPQVKRSSTETINLTNTFSMMKNPYALGFSLAIGLYVATEVAIYVWMP 240
           CLLLCWLAFRADYPQVKRSSTETINLTNTFSMMKNPYALGFSLAIGLYVATEVAIYVWMP
Sbjct: 181 CLLLCWLAFRADYPQVKRSSTETINLTNTFSMMKNPYALGFSLAIGLYVATEVAIYVWMP 240

Query: 241 SLLQEYQGDYTVLAAYALTIFFTLRAGGRFLGGWILNHFSWQQVMFWFSLAISLCYLGSM 300
           SLLQEYQGDYTVLAAYALTIFFTLRAGGRFLGGWILNHFSWQQVMFWFSLAISLCYLGSM
Sbjct: 241 SLLQEYQGDYTVLAAYALTIFFTLRAGGRFLGGWILNHFSWQQVMFWFSLAISLCYLGSM 300

Query: 301 LYGVEAAVILLPLSGLFMSMMYPTLNSKGISCFPVAQHGSVAGVILFFTAVSAALAPLCM 360
           LYGVEAAVILLPLSGLFMSMMYPTLNSKGISCFPVAQHGSVAGVILFFTAVSAALAPLCM
Sbjct: 301 LYGVEAAVILLPLSGLFMSMMYPTLNSKGISCFPVAQHGSVAGVILFFTAVSAALAPLCM 360

Query: 361 GLVGDIFGHVKYGFYLATGFAVLLCLLAGVNLIKDPSQALLSRETA 406
           GLVGDIFGHVKYGFYLATGFAVLLCLLAGVNLIKDPSQALLSRETA
Sbjct: 361 GLVGDIFGHVKYGFYLATGFAVLLCLLAGVNLIKDPSQALLSRETA 406


Lambda     K      H
   0.330    0.143    0.437 

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: 778
Number of extensions: 20
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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 (21.9 bits)
S2: 50 (23.9 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