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_4148 Glutamate-aspartate carrier protein

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4148
          Length = 443

 Score =  328 bits (840), Expect = 3e-94
 Identities = 174/404 (43%), Positives = 264/404 (65%), Gaps = 12/404 (2%)

Query: 15  VIVAIAIGILLGHFYPQTGV----ALKPLGDGFIKLIKMVIAPIIFCTVVSGIAGMQNMK 70
           +++ IA+G LL HF  +        L+P GD FI+LIKM++ PI+  +++ GIAG+ + K
Sbjct: 16  LVLGIALGALLNHFSAEKAWWISNVLQPAGDIFIRLIKMIVIPIVISSLIVGIAGVGDAK 75

Query: 71  SVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAY-VTAGKDQ 129
            +G+ G   +LYFE+V+TIA+++GL++ N  QPG+G  ID+STL    ++ Y  TA + Q
Sbjct: 76  KLGRIGLKTILYFEVVTTIAIVVGLLLANFFQPGSG--IDMSTLGTVDISKYQATAAEVQ 133

Query: 130 ---SIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGA-YGKPVLDFIDRFAH 185
              + +  ILN+IP+ I  A A G++L ++ FSV+FG  L  L +    P++      + 
Sbjct: 134 HEHAFIQTILNLIPSNIFAAVARGEMLPIIFFSVLFGLGLSSLQSDLRDPLVKMFQGVSE 193

Query: 186 VMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICR 245
            MF + +MIM+ APIG    +A T+  +G  SL+ L +L+I  Y+    F  VVLG I R
Sbjct: 194 SMFKVTHMIMQYAPIGVFALIAVTVANFGFASLLPLAKLVILVYVAIAFFAFVVLGVIAR 253

Query: 246 AHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLD 305
             GFSVLKL+R  ++EL++   T+SSE+ LPR++ KME  GA K++   V+PTGYSFNLD
Sbjct: 254 LFGFSVLKLMRIFKDELVLAYSTASSETVLPRVIEKMEAYGAPKAICSFVVPTGYSFNLD 313

Query: 306 GTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGH 365
           G+++Y ++AA+FIAQ     + I+ Q+ L+L L+++SKG AGV G  F+VL ATL +VG 
Sbjct: 314 GSTLYQSIAAIFIAQLYGIDLSISQQLLLVLTLMVTSKGIAGVPGVSFVVLLATLGSVG- 372

Query: 366 LPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDE 409
           +P+ GLA I G+DR M  AR   N++GNA+A +V+A+W    D+
Sbjct: 373 IPLEGLAFIAGVDRIMDMARTALNVIGNALAVLVIARWEGMYDD 416


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: 479
Number of extensions: 23
Number of successful extensions: 6
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: 443
Length adjustment: 32
Effective length of query: 412
Effective length of database: 411
Effective search space:   169332
Effective search space used:   169332
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