GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacG in Synechococcus elongatus PCC 7942

Align LacG, component of Lactose porter (characterized)
to candidate Synpcc7942_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like

Query= TCDB::P29824
         (273 letters)



>FitnessBrowser__SynE:Synpcc7942_0471
          Length = 276

 Score =  152 bits (385), Expect = 6e-42
 Identities = 83/263 (31%), Positives = 143/263 (54%), Gaps = 3/263 (1%)

Query: 12  IVQYSVLSLAAFLSIFPFIWMVIGTTNTTSQ-IIRGKVTF--GTALFDNIASFFAQVDVP 68
           ++ Y +L   A   + P +W+V     +  + I +    F       DN    + +  + 
Sbjct: 10  LLLYLLLGTIAVAMLIPLLWLVSTAFKSAGEDIFQFPPQFLPTQPTLDNFRRVWTENPLG 69

Query: 69  LVFWNSVKIALVGTALTLLVSSLAGYGFEMFRSKLRERVYTVILLTLMVPFAALMIPLFM 128
             F NS  +AL+   L LL  SLA Y       K R+ ++ +I+ T+++PF  +MIPL++
Sbjct: 70  QYFLNSTWVALLTVGLNLLFCSLAAYPLARLEFKGRQTLFLLIVATILIPFQVVMIPLYV 129

Query: 129 LMGQAGLLNTHIAIMLPMIASAFIIFYFRQASKAFPTELRDAAKVDGLKEWQIFFYIYVP 188
           L+   GL NT++ ++ P +ASAF IF  RQA +  P +L +AA++DG  +  +++ + +P
Sbjct: 130 LIINLGLRNTYLGLVFPYLASAFGIFLLRQAFQGIPKDLEEAARIDGCNDLGVWWNVMIP 189

Query: 189 VMRSTYAAAFVIVFMLNWNNYLWPLIVLQSNDTKTITLVVSSLASAYSPEYGTVMIGTIL 248
             R       + VF+ +W+++LWPLI+L   D  T+ L +++LAS +S ++  V  G++L
Sbjct: 190 SARPALITLAIFVFIGSWSDFLWPLIILDEPDRYTLPLGIATLASGFSLDWRLVAAGSVL 249

Query: 249 ATLPTLLVFFAMQRQFVQGMLGS 271
           + LP   VF A+QR  V     S
Sbjct: 250 SILPVFGVFLALQRYIVPSAAAS 272


Lambda     K      H
   0.331    0.140    0.416 

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: 244
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: 273
Length of database: 276
Length adjustment: 25
Effective length of query: 248
Effective length of database: 251
Effective search space:    62248
Effective search space used:    62248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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