GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Pseudomonas fluorescens FW300-N2C3

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate AO356_18980 AO356_18980 C4-dicarboxylate transporter

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_18980
          Length = 450

 Score =  626 bits (1614), Expect = 0.0
 Identities = 314/410 (76%), Positives = 369/410 (90%)

Query: 5   LFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGM 64
           L+KSLYFQV+ AIAIGILLGHFYP+ G  +KP GDGF+KLIKM+IAP+IFCTVV+GI GM
Sbjct: 7   LYKSLYFQVIVAIAIGILLGHFYPQTGVALKPFGDGFIKLIKMVIAPIIFCTVVSGIGGM 66

Query: 65  ESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQA 124
           ++MK+VG+TG  ALLYFEIVSTIAL+IGL++VNVVQPGAGM++D +TLD   +A +    
Sbjct: 67  QNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGAGMHIDVSTLDTSKIAGFISAG 126

Query: 125 KDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQV 184
           KDQ I+AFI++VIP +++GAFA+G+ILQVL+F+VLFGFALHRLG+ G+ + + I+ F+ V
Sbjct: 127 KDQSIIAFILNVIPNTIVGAFANGDILQVLMFSVLFGFALHRLGAYGKPVLDFIDRFAHV 186

Query: 185 IFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKA 244
           +F IINMIM+LAP+GAFGAMAFTIG YGVG+LVQLGQL+ICFYITC++FV++VLG+I +A
Sbjct: 187 MFIIINMIMKLAPLGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCVVFVLVVLGAICRA 246

Query: 245 TGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDG 304
            GFS+ K IRYIREELLIVLGTSSSESALPRML KME+LG +KSVVGLVIPTGYSFNLDG
Sbjct: 247 HGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLDG 306

Query: 305 TSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 364
           TSIYLTMAAVFIAQAT++ MD+ HQITLL+VLLLSSKGAAGVTGSGFIVLAATLSAVGHL
Sbjct: 307 TSIYLTMAAVFIAQATDTPMDLTHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGHL 366

Query: 365 PVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVL 414
           PVAGLALILGIDRFMSEARALTNLVGN VATIVVAKWVKELD  +L   L
Sbjct: 367 PVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWVKELDEDQLQTEL 416


Lambda     K      H
   0.327    0.142    0.401 

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: 687
Number of extensions: 19
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: 428
Length of database: 450
Length adjustment: 32
Effective length of query: 396
Effective length of database: 418
Effective search space:   165528
Effective search space used:   165528
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: 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