GapMind for catabolism of small carbon sources

 

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

Align sodium:C4-dicarboxylate symporter (dctA) (characterized)
to candidate Pf6N2E2_2249 Proton/glutamate symport protein @ Sodium/glutamate symport protein

Query= reanno::pseudo5_N2C3_1:AO356_18980
         (450 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2249
          Length = 420

 Score =  292 bits (748), Expect = 1e-83
 Identities = 172/408 (42%), Positives = 258/408 (63%), Gaps = 17/408 (4%)

Query: 17  VAIAIGILLG---HFYPQTGVALKPFG-------DGFIKLIKMVIAPIIFCTVVSGIGGM 66
           + IA+G+L+G   H +  +  + K          D F+++IKM+IAP++F T+V GI  M
Sbjct: 1   MGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLVFATLVGGIASM 60

Query: 67  QNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGAGMHIDVSTLDTSKIAGFISAG 126
            N +SVG+ G  A+ +F   S ++LLIG+ +VN+ QPGAG+++DV+   T+ +   ++ G
Sbjct: 61  GNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHATAAVP--VNTG 118

Query: 127 KDQSIIAFILNVIPNTIVGAFANGDILQVLMFSVLFGFALHRLGAYGKP-VLDFIDRFAH 185
            D S+ AFI +V P +I  A AN +ILQ+++FS+ FGFAL  +   G   + D I+  A 
Sbjct: 119 -DFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRITDCIEELAK 177

Query: 186 VMFIIINMIMKLAPLGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCVVFVLVVLGAICR 245
           VMF I + +M  AP+G F A+A  I   G+G LV  G+L+  FY+  ++   ++ GA   
Sbjct: 178 VMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILILWALLFGAGYL 237

Query: 246 AHGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLD 305
             G SV  L + IRE +L+   T+SSESA P+ +  +E+ GA K V   V+P GYSFNLD
Sbjct: 238 FLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFVLPLGYSFNLD 297

Query: 306 GTSIYLTMAAVFIAQATDTPMDLTHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGH 365
           G+ +Y   A +FIAQA +  +  T Q+ +LL L+++SKG AGV  +  +V+AATL  + +
Sbjct: 298 GSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMVTSKGMAGVARASVVVVAATL-PMFN 356

Query: 366 LPVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWV--KELDEDQ 411
           LP AGL LI+GID+F+  AR  TN+VGN++AT VVAK    +E DED+
Sbjct: 357 LPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSEPHEEADEDE 404


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: 482
Number of extensions: 21
Number of successful extensions: 4
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: 450
Length of database: 420
Length adjustment: 32
Effective length of query: 418
Effective length of database: 388
Effective search space:   162184
Effective search space used:   162184
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