GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Pseudomonas fluorescens FW300-N2E2

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate Pf6N2E2_5707 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5707
          Length = 450

 Score =  784 bits (2024), Expect = 0.0
 Identities = 409/450 (90%), Positives = 423/450 (94%), Gaps = 6/450 (1%)

Query: 1   MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVV 60
           MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKP GDGFIKLIKMVIAPIIFCTVV
Sbjct: 1   MTTRQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPFGDGFIKLIKMVIAPIIFCTVV 60

Query: 61  SGIAGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVA 120
           SGI GMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVN+VQPG GMHIDVSTLD SK+A
Sbjct: 61  SGIGGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNIVQPGVGMHIDVSTLDTSKIA 120

Query: 121 AYVTAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFI 180
            ++ A KDQSI+ FILNVIPNTIVGAFANGDILQVLMFSV+FGFALHRLGAYGKPVLDFI
Sbjct: 121 GFINASKDQSIIAFILNVIPNTIVGAFANGDILQVLMFSVLFGFALHRLGAYGKPVLDFI 180

Query: 181 DRFAHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVL 240
           DRFAHVMF IINMIMKLAPIGA GAMAFTIGAYGVGSLVQLGQLMICFYITCV+FVLVVL
Sbjct: 181 DRFAHVMFIIINMIMKLAPIGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCVVFVLVVL 240

Query: 241 GAICRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGY 300
           GAICRAHGFSV+KLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGY
Sbjct: 241 GAICRAHGFSVVKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGY 300

Query: 301 SFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360
           SFNLDGTSIYLTMAAVFIAQATDT MD+THQITLLLVLLLSSKGAAGVTGSGFIVLAATL
Sbjct: 301 SFNLDGTSIYLTMAAVFIAQATDTPMDLTHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360

Query: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELASGG 420
           SAVG LPVAGLALILGIDRFMSEARALTNLVGNAVAT+VVAKWVKELDEDQLQ ELASGG
Sbjct: 361 SAVGTLPVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWVKELDEDQLQTELASGG 420

Query: 421 RAISDTREEDD------LGVAEGPTPTTVK 444
           R I+D RE+D+      +  AE   P TVK
Sbjct: 421 RGIADVREDDEQIAAAQIAAAESSAPVTVK 450


Lambda     K      H
   0.326    0.142    0.402 

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: 796
Number of extensions: 23
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: 444
Length of database: 450
Length adjustment: 33
Effective length of query: 411
Effective length of database: 417
Effective search space:   171387
Effective search space used:   171387
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 (21.6 bits)
S2: 51 (24.3 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